In order to increase the efficiency of waxy maize breeding and classify heterosis groups of waxy maize, using specific locus amplified fragment sequencing(SLAF-seq) technology, it was conducted that evolutionary tree analysis, principal component analysis, population genetic structure analysis of 127 waxy germplasm maize inbred lines. In consideration of sib-lines and variety, in-depth mutual confirmation analysis was conducted. The results showed that the total of 1129131 SLAF tags and 754601 polymorphic SLAF tags were obtained; 60968 valid SNP markers were identified; minor allele frequency(MAF) average value was 0.18 and range was 0.05-0.5; polymorphic information content(PIC) average value was 0.26 and range was 0.09-0.38; genetic similarity(GS) among inbred lines average value was 0.7783 and range was 0.7310-0.9638. Combining evolutionary tree analysis with population genetic structure analysis, 127 waxy germplasm maize inbred lines were divided into temperate and tropical heterosis groups. Temperate heterosis group was divided into four subgroups, while tropical heterosis group was divided into three subgroups. In 33 pairs of sib-lines, 30 pairs of sib-lines GS were more than 75% GS among all inbred lines. In 12 varieties, the parents of 9 varieties belonged to temperate and tropical heterosis groups respectively. The parents of other 3 varieties belonged to tropical heterosis subgroups respectively. There was higher heterosis between temperate and tropical heterosis groups, while there was a certain heterosis among tropical heterosis three subgroups. The research provided theoretical guidance for combining of inbred lines and efficiency breeding.