A method of quality control of nucleic acid amplification, comprising a nucleic acid detection step and a determination step, wherein the nucleic acid detection step comprises the steps of: preparing a nucleic acid sample containing a target nucleic acid and a quality control polynucleotide; preparing a compartment containing one molecule of the target nucleic acid and a compartment containing one molecule of the quality control polynucleotide; and carrying out nucleic acid amplification of the target nucleic acid and the quality control polynucleotide, in the compartments, and carrying out signal detection using a detection probe to detect a signal originated from the detection probe, in the determination step, it is determined as to whether or not the nucleic acid detection step is proper on the basis of the result obtained in the signal detection step, the target nucleic acid contains a detection sequence, the quality control polynucleotide is a single-stranded polynucleotide which contains a first region, a second region and a third region, wherein the first region contains a sequence to which a first primer for target nucleic acid amplification can bind, the second region contains a sequence complementary to a sequence to which a second primer for target nucleic acid amplification can bind, and the third region contains one or both of the detection sequence and a sequence complementary to the detection sequence, a single-stranded polynucleotide which contains a sequence complementary to the sequence recited in item, or a double-stranded polynucleotide which contains both the polynucleotide recited in item and the polynucleotide recited in item, the detection probe contains a sequence complementary to the detection sequence, and the total number of the detection sequence and complementary sequence to the detection sequence in the quality control polynucleotide recited in item is different from the number of the detection sequence in the target nucleic acid. preparing a nucleic acid sample containing a target nucleic acid and a quality control polynucleotide; preparing a compartment containing one molecule of the target nucleic acid and a compartment containing one molecule of the quality control polynucleotide; and carrying out nucleic acid amplification of the target nucleic acid and the quality control polynucleotide, in the compartments, and carrying out signal detection using a detection probe to detect a signal originated from the detection probe, a single-stranded polynucleotide which contains a first region, a second region and a third region, wherein the first region contains a sequence to which a first primer for target nucleic acid amplification can bind, the second region contains a sequence complementary to a sequence to which a second primer for target nucleic acid amplification can bind, and the third region contains one or both of the detection sequence and a sequence complementary to the detection sequence, a single-stranded polynucleotide which contains a sequence complementary to the sequence recited in item, or a double-stranded polynucleotide which contains both the polynucleotide recited in item and the polynucleotide recited in item,