A fluorescent PCR method, a kit and a system for detecting methylation of a septin 9 gene in human peripheral blood free DNA on the basis of an ARMS-PCR method are disclosed. The method includes the following steps: (A) performing transition treatment to a CpG locus in the human peripheral blood free DNA containing the septin 9 gene, so that the non-methylated CpG locus is converted into UpG; (B) with the human peripheral blood free DNA after the transition treatment as a template, performing a fluorescent PCR reaction, wherein the fluorescent PCR reaction system includes: a specific primer and a probe sequence thereof for detecting the methylation of the septin 9 gene, a Taq enzyme, a UNG enzyme, dNTPs, dUTP, Mg<2+>, a PCR buffer solution, a first additive and a second additive, the first additive including bovine serum albumin and the second additive including dimethyl sulfoxide, NH4Cl and a sorbitol water solution. The method can avoid false positive phenomenon that methylation of only one CpG locus represents the methylation level of the whole gene. The method reduces detection limit of the methylation level to 1%, and has high sensitivity.