Bats are critical viral reservoirs that harbor viromes with high cross-species transmission risks, yet their virome diversity in the mainland Southeast Asia and adjacent regions remains underexplored. Here, we characterized the bat viromes from 659 samples (197 individuals, 16 species) from Yunnan province and Guangxi Zhuang autonomous region, China, as well as from Cambodia, using next-generation sequencing (NGS). RNA sequencing, viral classification, phylogenetic analyses, and deep learning-based host adaptability analysis were performed to reveal the viral composition and cross-species transmission risks. We identified 137 viral strains, including 40 novel species spanning 18 families. Viral richness was highest in Vespertilionidae bats (12 viral families found) along China’s southwestern border, where Middle Eastern respiratory syndrome (MERS)-like coronavirus (CoV) was found. Cambodian bat viruses were evolutionarily more distant from those of known viruses. A porcine epidemic diarrhea virus (PEDV)-related CoV was found in Cambodia, showing 90.36% genome homology with PEDV CV777 and exhibiting recombinant features between Suidae-adapted ORF1ab and Chiroptera-adapted Spike genes, suggesting that bats are the evolutionary source of PEDV. These findings illuminate the undercharacterized bat viral diversity in biogeographic transition zones and highlight the mainland Southeast Asia and adjacent regions as a hotspot for CoV recombination. We advocate for enhanced One Health-aligned surveillance targeting viral recombination hotspots and human–bat interfaces in this ecologically critical region.