Objective To discuss the rules of using traditional Chinese medicine (TCM) to treat systemic lupus erythematosus (SLE) and Sjögren syndrome (SS). Methods The TCM prescriptions for patients with SLE or SS treated at the Department of Rheumatology of Longhua Hospital, Shanghai University of Traditional Chinese Medicine between January 2013 and July 2021 were collected. The prescriptions collected were broken down and analyzed for frequencies of the efficacies, properties, flavors and meridian tropisms of drugs in the prescriptions. The correlation and clustering analysis was performed in VOSviewer software. Results The medication information of 3689 cases of inpatients was included, from which 69167 pieces of data of using TCM prescriptions were extracted. The top 20 high-frequency drugs for treating SLE patients were mainly drugs for promoting blood circulation and removing blood stasis, qi-tonifying drugs, and drugs for heat clearing and detoxicating, which were mostly sweet, bitter or acrid in flavor, cold, warm or neutral in properties, and of the spleen, liver or stomach meridian. The drugs could be seperated into 3 clusters, the blue cluster mainly included qi-tonifying drugs, blood-tonifying drugs, and drugs for promoting blood circulation and removing blood stasis; the green cluster mainly included drugs for heat clearing and drugs for promoting blood circulation and removing blood stasis; and the red cluster mainly consisted of drugs for promoting blood circulation and removing blood stasis, drugs for inducing diuresis and alleviating edema, drugs for dispelling wind-heat, and digestant drugs. The top 20 high-frequency drugs for treating SS patients were mainly drugs for promoting blood circulation and removing blood stasis, qi-tonifying drugs, and drugs for inducing diuresis and alleviating edema, which were mostly sweet, bitter or acrid in flavor, slightly cold, cold or warm in properties, and of the spleen, stomach or liver meridian. The drugs could be seperated into 2 clusters, the green cluster mainly consisted of yin-tonifying drugs, drugs for promoting blood circulation and removing blood stasis, and drugs for heat clearing; the red cluster mainly included qi-tonifying drugs, drugs for promoting blood circulation and removing blood stasis, and drugs for inducing diuresis and alleviating edema. Conclusions The medication for SLE is in line with the treatment principle of “supplementing qi and nourishing yin, detoxicating and removing stasis”; the medication for SS, on the other hand, agrees with the basic rule of “nourishing yin and clearing away heat, promoting body fluid to moisten dryness”. Both are based on the approach of strengthening the body resistance, which is in line with the diagnostic and treatment ideas of rheumatology department and may offer the ideas of TCM syndrome differentiation for clinical use of drugs and thereby guiding the current clinical practice.