The invention discloses a multi-methylation specific PCR primer design method and system. The method comprises the steps: setting parameters according to user requirements, designing and screening primers for a target methylation site, pairing the screened multiple methylation site primer pairs in pairs, checking the compatibility, selecting a maximum number of compatible multiple primer combinations, evaluating the designed multiple primer combinations, and determining whether the primers need to be redesigned. According to the invention, multi-methylation specific PCR primer design of a super-long sequence can be realized, secondary structures such as dimer/hairpin and the like between the interiors of a single pair of primers and between multiple pairs of primers can be effectively reduced, and non-specific amplification in a genome can be effectively reduced, the designed primers are high in specificity, the operability and accuracy of the multiplex methylation specific PCR experiment testing process are improved, and the working efficiency is greatly improved.