Objective To explore the effect of the independent inquiry-based teaching method in the experimental teaching of medical organic chemistry under the Internet plus. Methods From March 2019 to July 2022, all 815 undergraduates from the grade 2019-2022 of clinical medicine, preventive medicine and psychology in the Air Force Medical University were recruited, of which 610 students from the 2020-2022 class were the experimental group using inquiry-based teaching, whereas 205 students from the 2019 class were the control group using traditional teaching method. The teaching effects were evaluated through assessments and questionnaires. T-test and chi-square test were used for data analysis. Results In the final examination,the progress of the experimental group was higher than that of the control group [(86.77±1.64) vs. (80.28±4.26), P<0.05]. The process evaluation and summative assessment scores of the experimental group were higher than those of control group [(86.98±1.45) vs. (81.16±2.27), (85.27±1.53) vs. (79.43±5.17), all P<0.05]. The results showed that the students in the experimental group believed that this teaching method improved their ability to analyze problems [552(90.5%)], solve problems [534(87.5%)], collaborate [545(89.3%)] and hands-on skills [547(89.7%)], while the corresponding data of the control group were 131(63.9%), 168(82.0%), 144(70.2%) and 146(71.2%). The differences between the two groups were statistically significant (all P<0.05). Conclusions Investigative teaching is more conducive to students learning to learn, and to integrate data, analyze, problem-solve, as well as to enhance the interactive effect of "teaching" and "learning", to a certain extent to improve the quality and efficiency of medical organic chemistry teaching.