The invention discloses a high throughput sequencing method for detecting genes of multiple mutant types and applications thereof, and belongs to the field of gene detection. By searching database, variation sites of genes for a cancer target treatment, chemotherapy drug resistant genes, and chemotherapy drug sensitive genes, 100 bp of downstream of the variation sites, and 100 bp of upstream of the variation sites are taken as a target section; a capture probe matched with the target section is synthesized, the target area of DNA of a sample is captured, a high throughput sequencing library is established; then high throughput sequencing is carried out to obtain the sequence of a target section; and the results of cancer related gene mutation, insertion mutation, delete mutation, mutationof copy number, and gene fusion mutation can be obtained. The provided method can detect multiple kinds of mutations of 105 cancer related genes at a time and has the characteristics of high capturing efficiency and good uniformity.