Objective To investigate the current situation of clinical research paper writing and training needs of residents, and to provide reference for the development of clinical research training programs for residents. Methods Residents participating in the standardized training of residents at Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, from 2019 to 2021 were selected as the study subjects, and the questionnaire survey method was used to analyze the current situation of clinical research paper writing and training needs in April 2022. Descriptive statistics were used to analyze the relevant data. Results A total of 181 questionnaires were sent out and all of them were effectively returned, of which 106 (58.6%) had working experience; 32 (17.7%) had published or assisted others to publish clinical papers; 140 (77.3%) consulted their supervisors when they found clinical research problems; 106 (58.6%) used general search engines; 56 (30.9%) used Pubmed and other professional medical search engines; 51 (28.2%) went to the library, and 55 (30.4%) had only ever thought of publishing a clinical paper. A total of 110(60.8%) found each part of the paper difficult; however, 81(44.8%) also wished they could have done all the writing of the paper. 89(49.2%) could distinguish between retrospective and prospective studies; 141(77.9%) would use software to insert references. Only 25(13.8%) had received thesis training or lectures, but 160(88.4%) had a need for clinical thesis training in terms of specific training methods such as online lectures [130(71.8%)], one-on-one small-group tutorials [102(56.4%)], offline exchanges [83(45.9%)], self-study mainly with email or WeChat questions [28(15.5%)]. Conclusions Residents have severe deficiencies in the overall knowledge structure, methodology, and statistics of clinical dissertations, but subjectively there is a need for training and a positive attitude, and currently the clinical supervising physicians do not give enough attention and time to invest in training and counseling. In this regard, training centers and supervising physicians should increase the proportion of clinical research training and explore effective training programs.