In order to enhance the efficiency of waxy maize breeding and classify heterosis groups， specific-locus amplified fragment sequencing （SLAF-seq） technology was employed to perform phylogenetic analysis， principal component analysis， population genetic structure analysis on 127 waxy maize inbred lines. Further mutual validation was carried out using sibling lines and registered variety. The results revealed a total of 1129131 SLAF tags including 761467 polymorphic SLAF tags. A set of 60968 high-quality SNP markers were identified， with an average minor allele frequency （MAF） of 0.18 （range： 0.05-0.50） and an average polymorphic information content （PIC） of 0.26 （range： 0.09-0.38）. The average genetic similarity coefficient （GS） among inbred lines was 0.7783， ranging from 0.7310 to 0.9638. Based on integrated phylogenetic and population structure analysis， the 127 waxy maize inbred lines were classified into temperate and tropical heterosis groups. The temperate group was further divided into four subgroups， while the tropical group was divided into three subgroups. Among 33 pairs of sibling lines， 30 exhibited GS values exceeding 75% of the overall GS distribution across all inbred lines. Of the 12 varieties examined， the parents of nine varieties belonged to temperate and tropical heterosis groups， respectively， whereas the parents of the remaining three varieties were derived from different subgroups within the tropical heterosis group. These finding indicate that stronger heterosis occurs between temperate and tropical groups， while moderate heterosis exists among the three tropical subgroups. Collectively， this study provides a theoretical foundation for rational parental line combination and efficiency breeding in waxy maize.