The invention belongs to the field of gene data processing technology, and particularly relates to a whole genome association analysis method, a system and electronic equipment. The whole genome association analysis method comprises the steps of a, performing SNP site determining on original sequencing data of a sample, and obtaining SNP site information of the sample; b, establishing a coordinateaxis based on reference genome SNP information, and performing characteristic extraction on the SNP site information of the sample according to the coordinate axis based on the reference genome SNP information, and obtaining a characteristic vector of the sample; and c, clustering the characteristic vectors of the sample, obtaining the representative vectors of the sample, and combining the representative characteristic vectors for obtaining a non-redundancy sample. According to the method, through clustering the original data, characteristic expression of the sample is performed, and important characteristics are found, thereby reducing data computing amount; according to the similarity between the samples, the samples with high similarity are combined, and the rest samples are removed,thereby greatly reducing a memory requirement and improving efficiency.