Beans are a rich source of phosphatidylcholine (PC). This study aims to explore natural PC sources rich in polyunsaturated fatty acid (PUFA) with nutritional interest. PCs from six beans were purified (purity > 98.2%) by thin layer chromatography (TLC), and subsequently identified by ultra-high performance liquid chromatography-Quadrupole (Q)-high-resolution mass spectrometry (UHPLC-Q-HRMS). Results showed that the PC content of chickpea (Cicer arietinum) and soybean (Glycine max) was 50.0 and 34.0 mg/g, respectively, which was significantly higher than that of other beans (P < 0.05). Gas chromatographic analysis showed that soybean contained high proportion of PUFA (58.78%), and chickpea contained high proportion of docosahexaenoic acid (DHA) (2.73%). A total of 49 molecular species were identified by UHPLC-Q-HRMS. (18:2-18:2)PC was predominant in soybean, adzuki bean, runner bean, and common bean. (16:0-18:1)PC was the major species of chickpea PC, and many ether PC species and DHA-PC were identified. Discriminatory analysis by principal component analysis (PCA) indicated that the molecular profiles of chickpea PC were significantly different from other beans studied. The findings suggest that chickpea appears to be an interesting plant source of DHA and ether lipids for dietary supplement.