Whole exome sequencing (WES) technology has become a prevalent methodology in the field of human genetics research, providing an effective and affordable alternative to identify causative genetic mutations in genomic exon regions. This study focuses on the comparative assessment of four commercially available WES platforms on the DNBSEQ-Series sequencer, a platform that has not been extensively evaluated in the literature. The study provides a comprehensive comparison of data quality, capture specificity, coverage uniformity and variants detection accuracy across these platforms. The results indicate that these platforms exhibit comparable reproducibility and superior technical stability and detection accuracy on the DNBSEQ-T7 sequencer. Furthermore, the study establishes a robust workflow for probe hybridization capture that is compatible with the four commercial exome kits and the DNBSEQ-Series sequencer, offering uniform and outstanding performance, thus enhancing broader compatibility regardless of probe brand. This study contributes to filling a significant gap in the literature regarding the performance evaluation of WES platforms on the DNBSEQ-Series sequencer and provides valuable insights for researchers in human genetics research.The online version contains supplementary material available at 10.1186/s12864-025-12104-9.