Pharmacogenomics is an essential means to achieve personalized medicine. Multi-gene and multi-loci panel testing is an inevitable trend in its development, comprehensively analyzing the impact of genes on medications from the perspective of drug metabolism, efficacy, and adverse reactions, thereby formulating individualized regimen plans. Based on the requirements for detection throughput, nucleic acid mass spectrometry with medium throughput has become a suitable platform for pharmacogenomic testing. In this review, we examine the application of this technology in clinical pharmacogenomics, discuss its current challenges, and put forward suggestions for advancing its clinical application and precision medicine.