To explore and evaluate the long-term effects of diverse online teaching methods to minimize the negative influences of online teaching of basic courses in clinical medicine during the COVID-19 pandemic. Forty-nine students in grade 2017 majoring in clinical medicine (five-year program) were enrolled in this study (study group). They received online teaching of six basic clinical courses, including diagnostics, basic clinical skills, general surgery, medical imaging, and doctor‒patient communication, from March to July 2020. The study first introduced the process of online teaching, especially basic clinical skills such as history taking, physical examination, internal punctures, electrocardiography and so on. Then, they reviewed the schedules to reinforce these skills when the students returned to school. The final exam scores of four clinical courses, including internal medicine, surgery, obstetrics and gynaecology, and paediatrics, and the scores of graduation examinations were used to evaluate the long-term effects of online teaching. These scores were compared with students in grade 2014 who learned through offline teaching (control group). After graduation examinations, questionnaires were distributed to understand the influence of online teaching on learning clinical courses, internships and postgraduate entrance examinations. The results showed that the scores of internal medicine part I and surgery part II in the study group were higher than those in the control group, and the differences were statistically significant (P < 0.05). Differences were not statistically significant in scores of internal medicine part II, surgery part I, obstetrics and gynaecology, and paediatrics between the two groups (P > 0.05). Two students postponed graduation in grade 2017, so 47 students took part in the graduation examination. The scores for knotting, dressing change, and cardiopulmonary resuscitation in the study group were significantly lower than those in the control group (P < 0.05). For the three items internal punctures, four-step palpation in obstetrics, and assessment of children's growth and development, the scores in the study group were higher than those in the control group, and the differences were statistically significant (P <0.05). There were no statistically significant differences between these two groups in the three items of history taking, physical examination and disinfection (P > 0.05). All 47 participants in the study group completed the questionnaire survey, with a response rate of 100%. Twenty students thought that the online learning experience had a great influence on learning clinical courses such as internal medicine, surgery, obstetrics and gynaecology and paediatrics, whereas 27 students thought it had a slight influence. There were 23 students who thought online learning had a great influence and 24 students who thought it had a slight influence when attending the internship qualification examination. Thirteen students thought that the influence on the internship was great, 30 students thought it was slight, and 4 thought that online learning had no influence. Regarding which course had the most influence on the internship, 36 students thought it was diagnostics, 7 students thought it was general surgery, and 3 students thought it was other courses. Among the 40 students who participated in the entrance examination for a master's degree, 2 thought the online learning experience had a great influence, 19 thought it had a slight influence, and 11 students thought it had no influence. Among the six courses that influenced the re-examination for postgraduate students, 16 students thought the most influential course was diagnostics, 5 students chose general surgery, and 1 student thought it was another course. Exploration of diverse online teaching methods is helpful and successful for mastering clinical knowledge. However, online teaching had a great influence on some basic clinical skills that require more practice. The strategy used to reinforce these skills after returning to school makes up for the shortage of these practical skills in online courses to a certain extent.