The invention discloses a method for identifying varieties of aedes based on PCR-MS (polymerase chain reaction-mass spectrum) scanning. The method comprises the following steps: constructing an aedesvariety identification gene database (COI, COII, 28s, CytB400); constructing an aedes variety identification DNA (deoxyribonucleic acid) two-dimensional code, designing multiple PCR-MS primers, and performing multiple PCR-MS scanning; and performing analysis on thousands of gene sequences of nine aedes varieties, so as to obtain specific SNP (single nucleotide polymorphism) loci of each aedes variety. According to the loci, specific SNP loci of two or more genes of each variety are selected, meanwhile, specific and non-specific loci of other varieties are referred and treated as an exclusive method, analysis software is designed to recognize basic groups of multiple loci, and varieties of aedes can be confirmed, so that the accuracy in identifying aedes varieties can be improved, and detection omission can be avoided.