Fructus Psoralea is widely used to treat osteoporosis and skin inflammatory diseases. Because of the side effects on the liver, renal and cardiovascular systems, it is processed to salt‐processed Fructus Psoraleae to meet the requirements of clinical use. However, the mechanisms involved in the transformation of the chemical components are unclear. In this study, ultra‐high‐performance liquid chromatography quadrupole time‐of‐flight mass spectrometry was used to analyze the chemical profiles of this herbal medicine and the chemical transformation mechanism involved during the salt processing was studied. A total of 83 compounds were identified. Principal component analysis and orthogonal partial least squares discriminate analysis were used to observe the distribution trend of all samples and visualize the difference. Raw and processed Fructus Psoraleae were clearly clustered into two groups. Furthermore, 17 marker compounds were identified as primary contributors to their differences based on t‐test analysis (p < 0.01) and orthogonal partial least squares discriminate analysis (variable importance for the projection > 1). Finally, ultra‐high performance liquid chromatography coupled with triple quadrupole tandem mass spectrometry was used to evaluate the quality of Fructus Psoraleae by simultaneous analysis of 13 components highly related to efficacy. There were variations in the contents of 13 chemicals of Fructus Psoraleae and salt‐processed products. The results of untargeted and targeted metabolomics revealed that salt processing affected the chemical composition of Fructus Psoraleae.