The invention discloses a method for identifying SNP in an individual in Sanger sequencing oriented to PCR products of diploid. According to the method, firstly, fluorescent data of four bases of adenine A, guanine G, cytosine C and thymine T contained in a chromatogram map are independently separated, filtering and noise reduction processing is carried out on the separated fluorescent data by adopting a small wave multiscale analysis method; the waveform characteristics of the fluorescent data of the four bases are further analyzed, a first peak and a second peak of the waveform are detected, and the peak distance, the height specific value and the fluctuation degree specific value of the waveform characteristics are selected as the elements for judging SNP loca, a BP nerve net with the structure of 3-10-1 is selected as a classifier for the detection of the SNP loca, and training is carried out on the BP nerve net by adopting a Levenberg Marquardt algorithm; output is mapped as SNP evaluation scores from 0 to 100 by adopting piecewise linear transformation, the classification of the SNP loca is defined from a 1 level to a 5 level according to the evaluation scores, and the SNP confidence coefficient of the loca is judged according to the classification. The method for identifying the SNP in the individual in the Sanger sequencing oriented to the PCR products of the diploid can effectively detect the SNP loca in the individuals in sequencing files.