Objective To analyze the hospitalization expenses and structure of day surgery diseases between general hospital and traditional Chinese medicine hospital, so as to provide a basis for the reform policy formulation of the payment mode of traditional Chinese medicine medical insurance and the optimization of hospital management. Methods Relevant data such as hospitalization expenses and expenses structure of day surgery of one general hospital and one traditional Chinese medicine hospital in Shanghai between January 1, 2019 and June 30, 2022 were selected. The hospitalization expenses and expenses structure of day surgery in traditional Chinese medicine hospital and general hospital were analyzed. Results A total of 95232 day surgery cases were selected in the case hospitals, including 1389 cases in traditional Chinese medicine hospital and 93843 cases in general hospital. The age of day surgery patients in traditional Chinese medicine hospital was smaller than that in general hospital (P<0.001). The total hospitalization expenses [4379.6 (2293.2, 7563.4) vs. 7629.5 (4467.5, 14154.0) yuan], drug expenses [343.0 (65.0, 1107.0) vs. 749.0 (64.0, 1419.0) yuan], consumables expenses [858.8 (162.2, 1630.1) vs. 1951.0 (620.1, 5720.7) yuan], technical labor expenses [1994.8 (1116.8, 3252.4) vs. 3943.3 (2510.8, 6123.4) yuan] of day surgery patients in traditional Chinese medicine hospital were lower than those of patients in general hospital (P<0.001), and the examination expenses were higher than those of patients in general hospital [432.0 (0.0, 898.5) vs. 40.0 (0.0, 418.0) yuan, P<0.001]. In terms of the total hospitalization expenses structure of patients undergoing day surgery, the proportion of technical labor expenses in traditional Chinese medicine hospital was the highest (42.5%), and the proportion of consumables expenses in general hospital was the highest (43.7%). The specialty of day surgery in the traditional Chinese medicine hospital mainly focused on gynecology, general surgery, anorectal surgery and pain medicine, with the highest average expenses in ophthalmology. The specialty of day surgery in the general hospital mainly focused on urology, biliary, pancreatic and gastrointestinal surgery, ophthalmology and gynecolog, with the highest average expenses in orthopedics. There was no statistically significant difference between the age of patients undergoing hemorrhoidectomy in traditional Chinese medicine hospital and that in general hospital (P>0.05). The total hospitalization expenses [7177.4 (6057.5, 8225.7) vs. 10730.3 (8895.7, 14291.4) yuan], drug expenses [838.0 (441.0, 1342.0) vs. 1532.0 (1335.0, 1698.0) yuan], consumables expenses [4518.7 (4268.3, 5084.9) vs. 5550.9 (4066.6, 8340.7) yuan], technical labor expenses [1138.8 (911.3, 1414.2) vs. 3793.9 (2997.1, 4410.3) yuan] of day surgery patients undergoing hemorrhoidectomy in traditional Chinese medicine hospital were lower than those of patients in general hospital (P<0.05), and the examination expenses were higher than those of patients in general hospital [329.0 (0.0, 598.0) vs. 40.0 (40.0, 40.0) yuan, P<0.05]. In terms of the total hospitalization expenses structure of day surgery patients undergoing hemorrhoidectomy, the highest proportion was consumables expenses both in traditional Chinese medicine hospital and general hospital (63.8% and 53.6%, respectively). Conclusions There are differences between the hospitalization expenses of day surgery in traditional Chinese medicine hospital and general hospital. The dominant disease types of day surgery in traditional Chinese medicine hospitals need to be further cultivated. In the future, when the traditional Chinese medicine medical institutions implement the payment according to the diagnosis-related group/diagnosis-intervention packet, they should fully combine the actual situation of the medical institutions and the characteristics of the disease type, and at the same time, they need to further establish the medical fine management based on the disease type quality evaluation.