Objective To investigate the healthcare system reform in traditional Chinese medicine (TCM) hospitals in Sichuan and analyze the existing issues at this stage. Methods All public TCM hospitals in Sichuan (a total of 210) were selected to collect information through the National Comprehensive Statistical Network Direct Reporting Information System for the investigation of the healthcare system reform. The survey was conducted in July 2024, and the data collection relied on the relevant information reported by the sample hospitals from January 1st to December 31st, 2023. This study only analyzed the basic situation, staffing, TCM services, and information technology construction of TCM hospitals. Results A total of 210 survey questionnaires were collected, with a 100% response rate. The survey revealed that licensed practitioners of TCM (including licensed assistant practitioners) accounted for 59.2% of the total number of licensed practitioners, and TCM professional and technical personnel accounted for 50.4% of the total number of pharmaceutical professional and technical personnel. The median number of TCM medical technology projects carried out by the surveyed institutions was 52, the median proportion of outpatient TCM medical service income to outpatient medical income was 8.6%, and the median proportion of inpatient TCM medical service income to inpatient medical income was 13.7%. The proportion of discharged patients primarily treated with TCM was 30.6%, and the coverage rate of TCM-dominant disease types among inpatients in TCM medical institutions was 44.8%. A total of 52 institutions (24.8%) had achieved interconnectivity between prescription information and retail pharmacies, while 158 institutions (75.2%) had not. Among tertiary medical institutions, 67 had achieved level 4 in electronic medical record application functionality, while 32 were at level 3 or below. Conclusions After years of in-depth healthcare system reform, the construction and services of TCM hospitals in Sichuan have seen some development. However, there are still some shortcomings, such as insufficient TCM talent allocation, low utilization rate of TCM medical technology, unclear characteristics of TCM treatment, and low level of electronic medical record informatization. Therefore, it is necessary to further strengthen the cultivation and introduction of TCM talents, vigorously develop TCM characteristics, promote informatization construction, and promote the inheritance, innovation, and high-quality development of TCM.