Objective To explore the clinical application of NeoSeq in newborn screening. Methods Based on the results obtained from traditional newborn screening (NBS), three cohorts were recruited into the present study: 36 true positive cases (TPC), 60 false-positive cases (FPC), and 100 negative cases. The dried blood spots of the infants were analyzed with NeoSeq, which is based on multiplex PCR amplicon sequencing. Results Overall, the sensitivity of both NeoSeq and traditional NBS projects was 55.6% (20/36) in the detection of TPC. NeoSeq detected disease-related genes in 20 of 36 TPC infants, while it could not identify these genes in eight children. Five cases (3.1%) with disease risk were found in the FPC and NC cohorts. There was a significant time difference in the diagnostic result cycles between the two methods − 10 days for NeoSeq vs. 43 days for traditional NBS. Conclusions NeoSeq is an effective method of genomic sequencing for newborn screening. It can detect most inborn errors of metabolism, reduce the rate of false positive results, shorten the reporting cycles, and reduce the screening cost.