Disclosed are a method and system for genotyping a predetermined region in a nucleic acid sample. The method for genotyping the predetermined region in the nucleic acid sample comprises the following steps: using a primer set to amplify the nucleic acid sample to acquire an amplified product, where the primer set is specific to the predetermined region; building a sequencing library with respect to the amplified product; sequencing the sequencing library to acquire a sequencing result constituted by multiple pieces of sequencing data; determining the sequencing data from the predetermined region; and genotyping the predetermined region on the basis of the composition of the sequencing data from the predetermined region.