SummaryPrimary immune thrombocytopenia (ITP) is an acquired autoimmune disease. Cellular and systemic lipid metabolism plays a significant role in the regulation of immune cell activities. However, the role of lipoprotein lipids and apolipoproteins in ITP remains elusive. The automatic biochemistry analyser was used to measure the levels of serum total cholesterol (TC), triglyceride (TG), low‐density lipoprotein cholesterol (LDL‐C), high‐density lipoprotein cholesterol (HDL‐C), apolipoprotein A‐I (apoA‐I), apoB, apoE and lipoprotein a [LP(a)]. Genetic variants strongly associated with circulating lipoprotein lipids and apolipoproteins (LDL‐C, apoB, TG, HDL‐C and apoA‐I) were extracted to perform Mendelian randomization (MR) analyses. Finally, drug‐target MR and passive ITP mice model was used to investigate the potential druggable targets of ITP. Levels of HDL‐C, apoA‐I, decreased and LP(a) increased in ITP patients compared with healthy controls. Low HDL‐C was causally associated with ITP susceptibility. Through drug‐target MR and animal modelling, ABCA1 was identified as a potential target to design drugs for ITP. Our study found that lipid metabolism is related to ITP. The causative association between HDL‐C and the risk of ITP was also established. The study provided new evidence of the aetiology of ITP. ABCA1 might be a potential drug target for ITP.