Objective To investigate the differences in the serum levels of high-density lipoprotein2 cholesterol (HDL2-c) and high-density lipoprotein3 cholesterol (HDL3-c) in patients with rheumatoid arthritis (RA) and healthy controls, and to analyze the relationship between the levels of HDL2-c and HDL3-c and RA disease activity.Methods A total of 45 RA patients admitted to our hospital from January 2018 to December 2018 were selected as the RA group, and another 45 healthy individuals undergoing physical examination during the same period were enrolled as the control group. Fasting blood samples were collected from all the participants, and none of them had a history of cardiovascular diseases or diabetes mellitus and did not take any lipid-lowering drugs. The concentrated HDL2-c and HDL3-c were extracted by ultracentrifugation. The levels of HDL subcomponents between RA patients and healthy controls were compared to analyze the effects of disease activity on HDL2-c and HDL3-c. The differences in levels of HDL2-c, HDL3-c and other lipoproteins (TC, TG, LDL-c, HDL, ApoA-I and ApoB) between RA patients and healthy controls were analyzed using independent samples t test. The analysis of variance was performed to identify the effects of age and gender on HDL2-c and HDL3-c levels.Results Compared with the control group, the levels of TG and ApoB were higher, while the levels of HDL, HDL2-c, HDL3-c, and ApoA-I as well as HDL2/HDL3 ratio were lower in RA patients (P < 0.05). Among the healthy individuals, the levels of HDL2-c and HDL3-c in the female were higher than those in the male (P < 0.05). The DAS28 score affected the levels of HDL2-c in RA patients (P < 0.05). After adjusting for age, gender, disease duration, and glucocorticoid use, the concentration of HDL2-c decreased by 0.061 mmol/L when DSA28 score increased by 1 (P < 0.05). The levels of HDL2-c and HDL3-c were higher in RA patients with longer disease duration (P < 0.05).Conclusions The levels of HDL2-c and HDL3-c are decreased in RA patients, and the reduced concentration of HDL subcomponents, especially that of HDL2-c, may lead to an increased risk of cardiovascular diseases in women with RA.