The Tibetan–Yi Corridor, located on the eastern edge of the Tibetan Plateau, is the main route of the people of the plateau. Human settlement and diffusion along the corridor have played a pivotal role in shaping the genetic architecture of Sino-Tibetan-speaking (STs) populations in China. In this study, five STs groups (Chengdu Tibetan, Chengdu Han, Muli Tibetan, Lugu Lake Mosuo and Xichang Yi) settling in the Tibetan–Yi Corridor were genotyped via AGCU InDel 50 kit on the capillary electrophoresis platform to decrypt the genetic landscape and phylogenetic relationship of STs populations and investigate the forensic characteristics. Allele frequency distributions of all autosomal insertion/deletion polymorphisms (InDels) in studied groups comply with Hardy–Weinberg equilibrium. The combined power of discrimination values are 0.9999999999999999998, 0.9999999999999999995, 0.9999999999999999999, 0.999999999999999993 and 0.99999999999999999994, respectively, and all the combined probability of exclusion values exceed 0.9990. Forensically relevant statistics implied that these InDels could be used for individual identification and as a promising alternative to STR profiling in paternity testing. Typical population comparisons showed strikingly high homogeneity among studied STs people, indicating complicated genetic admixture among populations in the Tibetan–Yi Corridor. The STs groups in the Tibetan–Yi Corridor keep close genetic affinity with geographically or linguistically close populations, and the genetic components of investigated populations arose from a mixture of multiple ancestral gene pools (resulting from the admixture from the ancestral Highland Tibetans and ancestral Lowland indigenous populations).