Objective Quick TarSeq integrated system developed by our groups for on-field fast analysis is a fully automated and integrated system, which can be applied to the InDel ancestry inference, and complete the “sample-in result-out” rapid automatic InDel typing in about 2 h. In this paper, the performance of the InDel ancestry inference microfluidic chip amplification system was studied, hoping to provide a reference for practical application.Methods The system was validated by sensitivity, inhibitor tests, success rate, concordance tests, sizing precision and accuracy, peak height balance, case sample tests, and the accuracy of infering ancestral origins.Results The microfluidic chip amplification system was concordant with traditional methods, with 95.65% success rates and 98.85% concordance rates for 138 testing samples. The complete InDel profiles can be obtained from more than 5 ng of template DNA input. The best collection of buccal swab was the donor who performed 8 swipes inside of cheek. The best collection of dried blood spot samples was 6 pieces (Φ=2 mm). The average heterozygous peak height ratio across all locus was 0.86. The standard deviation of allelic ladder for 10 runs was within 0.3 bp. The size differences between allele and corresponding allele in allelic ladder was within 0.5 bp.Conclusion Microfluidic chip amplification system enable providing reliable InDel profiles from buccal swabs, dried blood spot, dried saliva spot samples and cigarette butt with accurately ancestral inference. It is possible to yield “sample-in result-out” results of InDel typing in 2 h. This system can meet the requirements of on-site testing and can be used for forensic casework.