The invention provides a method and system for identifying a Chinese population epithelial cell body fluid spot tissue source from the gene level. The method comprises the steps of utilizing a first PCR amplification primer set for performing first amplification on body fluid spot DNA, and obtaining a first amplification PCR product, wherein the first PCR amplification primer set is composed of nine pairs of amplification primers corresponding to nine genes of CYP2B7P1, MUC4, L.cri, HTN3, STATH, MUC7, LCE2B, DCD and CCL27 one to one; according to the gene expression condition in the first amplification PCR product, whether or not at least one of vaginal secretion, saliva and skin is contained in body fluid spots is judged. According to the scheme, the Chinese population body fluid tissue source can be effectively determined from the gene level, the step for identifying the body fluid or spot tissue source thereof at a criminal investigation site is greatly simplified, and the accuratescientific basis can be supplied to case character clearing, conviction and sentencing.