Background: Chinese Yunnan Hani group is an East Asian ethnic group mainly distributed in China, Thailand, Laos, Vietnam, and Burma. The genetic makeup of Chinese Yunnan Hani ethnic group remains to be further investigated. The insertion/deletion (InDel) polymorphism genetic markers are highlighted by their merits such as shorter amplified fragments, lower mutation rates, and are considered effective tools for population genetic investigations. Methods: The 221 individuals of Chinese Yunnan Hani group were enrolled to obtain the genetic data and polymorphic profiles of 57 autosomal InDels through multiplex amplification and genotyping. Population genetic analyses were performed between Chinese Yunnan Hani group and 30 global reference populations. Results: The forensic parameters, especially cumulative power of discrimination and combined probability of exclusion values, which were 0.9999999999999999999999968 and 0.999958, separately, illustrated that this novel InDel multiplex amplification system could be utilized as a powerful tool for personal identification and paternity testing in Chinese Yunnan Hani group. The results of population genetic analyses indicated that Chinese Yunnan Hani group showed relatively smaller genetic distances and similar genetic structures with the reference East Asian populations. Conclusions: The genetic polymorphisms and results of intercontinental population architecture differentiation analyses demonstrated the high efficiency of this novel InDel multiplex amplification system. The genomic data and findings of this research will contribute to the ongoing genetic exploration of Chinese Yunnan Hani group and increase our insights into the genetic architecture of worldwide populations.