Objective · To design and build a high-throughput sequencing approach based on targeted panel sequencing (TPS) using for the primary immunodeficiency disease (PID) diagnosis. Methods · By reviewing the literature and querying the relevant databases to determine the known disease-causing genes of PID, capture probes using for the TPS were designed and customized for all exons and flanking sequences of these genes. A child suspected with PID was diagnosed by the customized TPS. Results · The PID sequencing panel contains a total of 100 known pathogenic genes. The sequencing data of the patient has 16 414 298 reads. The average coverage depth is 157 X, 98.35% of the target region sequencing depth is greater than 20 X, and 99.97% of the target region sequencing depth is greater than 1 X. Finally, a heterozygous nonsense mutation was found in the exon 2 of the CXCR4 gene (c.1000C>T, p.Arg334*) in the child. The results of Sanger sequencing confirmed the variation in the child and showed that his parents were wild-type at the corresponding sites, indicating the mutation is de novo. Conclusion · This study established a high-throughput sequencing diagnostic approach for PID, with which a case of WHIM syndrome was successfully diagnosed.