A method for simultaneously detecting a plurality of target nucleic acids performed by an integrated real-time nucleic acid analysis system comprising a plurality of automated separation and purification instruments, a real-time nucleic acid amplifier, and a controller, the method comprising: 1) separating nucleic acids from various biological samples and purifying the separated nucleic acids, by the plurality of automated separation and purification instruments; 2) applying the purified nucleic acids to a plurality of reaction tubes, wherein the plurality of reaction tubes includes a first reaction tube for detecting a first target nucleic acid and a second reaction tube for detecting a second target nucleic acid different from the first target nucleic acid; 3) assigning wells of a multi-well temperature circulation block to the plurality of reaction tubes according to the target nucleic acid, wherein a first well is assigned to the first reaction tube and a second well is assigned to the second reaction tube, and storing information on the samples for each well of each of the group of wells; 4) loading each of the plurality of reaction tubes prepared in step 2) to a well corresponding to the information on the biological samples, wherein the first reaction tube is loaded to the first well and the second reaction tube is loaded to the second well; and 5) simultaneously amplifying the first target nucleic acid loaded on the first well and the second target nucleic acid loaded on the second well under a same thermal condition and performing at least one of qualitative analysis and quantitative analysis on the respective target nucleic acids separated from the plurality of biological samples, thereby to obtain amplification results, wherein a first primer set and a first probe is added to the first reaction tube for amplifying and detecting the first target nucleic acid, and a second primer set and a second probe is added to the second reaction tube for amplifying and detecting the second target nucleic acid, characterized in that: - in step 1) nucleic acids are also separated from standard samples; - in step 3) a first information on a standard sample and biological sample of the first reaction tube and a second information on a standard sample and biological sample of the second reaction tube is stored; and wherein the first and second primer sets and the first and second probes are different from each other and have a similar melting point such that simultaneously amplifying and analyzing the nucleic acids are performed under the same thermal conditions, and wherein the first target nucleic acid is separated from a first biological sample and the second target nucleic acid is separated from a second biological sample different from the first biological sample. 1) separating nucleic acids from various biological samples and purifying the separated nucleic acids, by the plurality of automated separation and purification instruments; 2) applying the purified nucleic acids to a plurality of reaction tubes, wherein the plurality of reaction tubes includes a first reaction tube for detecting a first target nucleic acid and a second reaction tube for detecting a second target nucleic acid different from the first target nucleic acid; 3) assigning wells of a multi-well temperature circulation block to the plurality of reaction tubes according to the target nucleic acid, wherein a first well is assigned to the first reaction tube and a second well is assigned to the second reaction tube, and storing information on the samples for each well of each of the group of wells; 4) loading each of the plurality of reaction tubes prepared in step 2) to a well corresponding to the information on the biological samples, wherein the first reaction tube is loaded to the first well and the second reaction tube is loaded to the second well; and 5) simultaneously amplifying the first target nucleic acid loaded on the first well and the second target nucleic acid loaded on the second well under a same thermal condition and performing at least one of qualitative analysis and quantitative analysis on the respective target nucleic acids separated from the plurality of biological samples, thereby to obtain amplification results, wherein a first primer set and a first probe is added to the first reaction tube for amplifying and detecting the first target nucleic acid, and a second primer set and a second probe is added to the second reaction tube for amplifying and detecting the second target nucleic acid, characterized in that: - in step 1) nucleic acids are also separated from standard samples; - in step 3) a first information on a standard sample and biological sample of the first reaction tube and a second information on a standard sample and biological sample of the second reaction tube is stored; and wherein the first and second primer sets and the first and second probes are different from each other and have a similar melting point such that simultaneously amplifying and analyzing the nucleic acids are performed under the same thermal conditions, and wherein the first target nucleic acid is separated from a first biological sample and the second target nucleic acid is separated from a second biological sample different from the first biological sample. - in step 1) nucleic acids are also separated from standard samples; - in step 3) a first information on a standard sample and biological sample of the first reaction tube and a second information on a standard sample and biological sample of the second reaction tube is stored; and