The invention discloses a method for removing a human gene sequence in macro genome sequencing data. The method comprises the following steps that a reference gene set is constructed through originalsequencing data of genome planning samples of thousands of people, and after high-quality sequencing read of genome data of thousands of people is obtained, genome assembly software assembles the sequencing read into a long gene segment to serve as a reference sequence later to be compared with the sequencing read; gene fragment data is extracted from all non-tumor samples from an NCBI database toserve as gene fragment data of an NCBI Bioproject for subsequent processing; the data of the genome data of thousands of people and the data of the NCBI Bioproject are merged, and after redundancy elimination, the data becomes a non-redundant gene fragment data set; virus genome sequences in the non-redundant gene fragment data set are found out and removed from the gene fragment sequence; the gene fragment sequence without the virus genome sequences serves as a reference genome for removing a human sequence in the macro genome sequencing data.