A substance detection system, characterized in that the substance detection system comprises: a reference crystal resonator and a detecting crystal resonator, formed on a single quartz substrate; an oscillation control portion configured for sequentially oscillating the reference crystal resonator and the detecting crystal resonator at a fundamental wave frequency and a third harmonic frequency; a frequency measuring portion configured to measure at least any of fundamental wave frequencies of the reference crystal resonator and the detecting crystal resonator and third harmonic frequencies of the reference crystal resonator and the detecting crystal resonator; a temperature identifying portion configured for identifying a surface temperature of the quartz substrate, based on a difference between a deviation of the fundamental wave frequency from at least any predetermined reference fundamental wave frequency of the reference crystal resonator and the detecting crystal resonator and a deviation of the third harmonic frequency from a predetermined reference third harmonic frequency; and a substance identifying portion configured for identifying a temperature at which a contaminant attached to the detecting crystal resonator is desorbed from the detecting crystal resonator, so as to identify the contaminant based on the temperature at which the contaminant is desorbed, and the temperature being identified based on at least any of a difference between the fundamental wave frequency of the reference crystal resonator and the fundamental wave frequency of the detecting crystal resonator or a difference between the third harmonic frequency of the reference crystal resonator and the third harmonic frequency of the detecting crystal resonator measured by the frequency measuring portion, and the temperature identified by the temperature identifying portion. a reference crystal resonator and a detecting crystal resonator, formed on a single quartz substrate; an oscillation control portion configured for sequentially oscillating the reference crystal resonator and the detecting crystal resonator at a fundamental wave frequency and a third harmonic frequency; a frequency measuring portion configured to measure at least any of fundamental wave frequencies of the reference crystal resonator and the detecting crystal resonator and third harmonic frequencies of the reference crystal resonator and the detecting crystal resonator; a temperature identifying portion configured for identifying a surface temperature of the quartz substrate, based on a difference between a deviation of the fundamental wave frequency from at least any predetermined reference fundamental wave frequency of the reference crystal resonator and the detecting crystal resonator and a deviation of the third harmonic frequency from a predetermined reference third harmonic frequency; and a substance identifying portion configured for identifying a temperature at which a contaminant attached to the detecting crystal resonator is desorbed from the detecting crystal resonator, so as to identify the contaminant based on the temperature at which the contaminant is desorbed, and the temperature being identified based on at least any of a difference between the fundamental wave frequency of the reference crystal resonator and the fundamental wave frequency of the detecting crystal resonator or a difference between the third harmonic frequency of the reference crystal resonator and the third harmonic frequency of the detecting crystal resonator measured by the frequency measuring portion, and the temperature identified by the temperature identifying portion.