An analysis system, an auxiliary analysis apparatus, and an analysis method are provided. The analysis method is used to perform a composition analysis operation on an analyte of a sample, and includes: a first heating step, a first mass spectrometry analysis step, a second heating step, a second mass spectrometry analysis step, and an analysis step. A heating device heats a non-analyzed area and a to-be-analyzed area of the sample in the first and the second heating step, respectively. In the first and the second mass spectrometry analysis step, gas generated after heating of the sample is guided into a gas chromatography-mass spectrometer, and two pieces of analysis data are correspondingly obtained. The analysis step is to compare the two pieces of analysis data and generate analysis result data. The analysis result data contains components of a composition that forms at least one portion of the analyte.