Cave burial is a funerary practice believed to be associated with modern Kra-Dai (KD) and Hmong-Mien (HM) speakers for thousands of years. However, the extent to which these ancient cave burial practitioners contributed to the formation of modern ethnic minority groups remains poorly understood due to the limited ancient genomic data. We generated 14 newly sequenced ancient human genomes from cave burial sites in Guangxi. The findings reveal continuous gene flow from northern lineages into ancient cave burial populations, shaping their genetic profiles over time. We observed a significant genetic distinction in HM populations: Southeast Asian HM groups derive 74.8% to 100% of their ancestry from cave burials, preserving a robust ancient southern genetic signature, while Chinese HM populations exhibit only 11.1% to 37.2% ancient cave burial ancestry, but heavily admixed with Yellow River-related populations (14.7% to 52.1%), reflecting differential historical interactions with northern migrants. In contrast, most KD speakers maintain tight genetic clustering with Guangxi ancestors (28.5% to 100% contribution from cave burials). The HM formation involved admixture between ancient cave burials, northern farmers, and local KD-related groups, which is evident in the genetic cline of She and Miao populations.