Island Southeast Asia (ISEA) remains consistently underrepresented in large-scale human genomic resources despite its rich ancestral and lifestyle diversity. The region's complex population history and environmental/pathogen pressures could have shaped its populations' unique immune responses, yet these have never been systematically characterized. Here, we generated single-cell PBMC profiles from 199 Indonesians sampled across four populations in the islands of Bali and New Guinea. These groups capture diversity in regional genetic ancestries (West ISEA-like and Papuan-like) and lifestyle contrasts (urban versus rural communities in Bali; highland versus lowland communities in New Guinea), providing a window into how ancestry and environment jointly shape immune variation across ISEA. We characterized cell type-specific proportions and gene expression, identifying both shared and cell type–specific expression quantitative trait loci (eQTLs); these include local ancestry–driven variants and overlaps with introgressed archaic haplotypes, including Denisovan-derived alleles. Using cell type–specific co-expression networks, we uncovered environment-associated expression modules, particularly in T cell subsets, that distinguish urban and rural cohorts. Paired TCR sequencing further revealed divergent adaptive immune repertoires aligned with these environmental differences. Together, this study provides the first large-scale single-cell immune atlas of ISEA, highlighting how ancestral and environmental diversity jointly shape human immunity in this globally important yet understudied region.