Objective Current forensic SNP genotyping methods often require imported platforms and are labor-intensive, time-consuming and costly. Droplet digital PCR (ddPCR) is a new generation of PCR technology that allows rapid qualification of rare target DNA sequence, and is less susceptible to PCR inhibitors. This study is intended to establish a SNP genotyping method on domestic ddPCR platform and explore the applicability of ddPCR in forensics.Methods Genotyping system of the high altitude adaptive EPAS1 haplotype (rs115321619, rs73926263, rs73926264, rs73926265 and rs55981512) was established by ddPCR. Then we tested the specificity of primers and probes, evaluated its accuracy, stability, sensitivity and adaptability separately. Meanwhile, ddPCR and SNaPshot minisequencing technology were compared in terms of inhibitor resistance ability. Finally, preliminary application in 70 samples were conducted.Results The ddPCR assay only required a total run time within 2.5 h, and showed high accuracy and repeatability in SNP genotyping. The detection sensitivity was 0.312 5 ng. DdPCR assays also exhibited better tolerance to inhibitors than SNaPshot. The tested individuals showed good consistence with their background information.Conclusion The SNP genotyping assay based on ddPCR is accurate, rapid, easily-used and shows great resistance to perturbations by inhibitors, which has strong application potential in the field of rapid forensic detection, and is suitable for forensic analysis.