Astragalus propinquus (known as Mongolian milkvetch in English and as huáng qí in Chinese) is commonly used in Traditional Chinese Medicine to treat chronic kidney diseases. The dominant contents of Astragalus propinguus were analyzed and choline was found to be one of the effective compounds for kidney disease treatment. In this study, the kidney protective effect of choline was examined in primary mouse proximal tubule cells and HEK cells. Lipidomic analysis showed that deoxysphingolipid (deoSL) levels were increased in the plasma from patients with chronic kidney disease (CKD), indicating deoSL as toxins in CKD. In vitro study revealed that palmitic acid (PA) induced increased levels of deoSL as well as intracellular ROS. Choline treatment attenuated such increases. The regulatory effect was mediated by organic cation transporter 2 (OCT2), as OCT2 overexpressing cells were protected from PA-induced toxicity. On the other hand, TNFa, which is commonly increased in chronic kidney disease, decreased OCT2 expression levels and reduced choline uptake in kidney proximal tubule cells. In summary, these results revealed a potential therapeutical role of Astragalus propinguus in the treatment of chronic kidney disease.