The domestic pig (Sus scrofa) and subfamilies have a long-term and extensive gene flow, especially in Southeast Asia. Demographically, as a gateway of southern China, Yunnan province with unique geographical location and complex climate system, but genomic, genetic introgression of Yunnan indigenous pigs is insufficient. Here, we analyzed population structure, differentiation, gene flow, adaptive introgression, signature selection and gene function of Yunnan indigenous pigs, European commercial and other Southeast Asia pigs using a pig genomics reference panel (PGRP v1) from pig Genotype-Tissue Expression project (PigGTEx). In this study, we clarified that the Diannan small-ear pig owned particular genetic information in the whole genome; we provided evidence of the introgression events from the Vietnam pig to the Diannan small-ear pig. We also outlined at least two conceptual routes of gene flow to Diannan small-ear in Southeast Asia. Three introgressed loci with similar chromosome positions and strong signature selection harbored the NAF1, NPY1R and NPY5R genes, which related to fat mass, immunity, and litter weight of pig complex trait using multiple bio-functionalization databases. Conclusively, these results laid the foundation for understanding introgression from Southeast Asia pigs to Yunnan indigenous pigs and provided a new insight into explaining the biological function of genes through multiple databases.