The invention relates to a method and system for analyzing a tumor mutation load based on high-flux targeted sequencing data. The method comprises the following steps that through high-flux targeted sequencing, sequences of selected exons and upstream and downstream areas of target genes in a tumor sample and a pairing contrast sample are subjected to sequencing; sequencing data obtained from thetumor sample and the pairing contrast sample is compared with a human reference genome sequence, and the number of mutated somatic cells in the sequences of the selected exons and the upstream and downstream areas of the target genes in the tumor sample is calculated; the mutation numbers of the somatic cells in the selected exons and the upstream and downstream areas of the target genes are addedto obtain a total mutation number, the lengths of the selected exons and the upstream and downstream areas of the target genes are added to obtain a total area length (Mb), and TMB is calculated through the following formula: TMB=the total mutation number/the total area length.