Objective To combine anatomage table technique of multi-touch virtual anatomy system (virtual autopsy table) with case-based teaching, and the evaluation was done in appendicectomy of surgical experiment. Methods A total of 72 subjects were selected from the 2015 class “5+3” clinical students of Fujian Medical University were divided into two groups. The students in the experimental group were used cooperate with multimedia and CBL case teaching +AT teaching method. The students in the control group used multimedia and CBL case teaching + traditional teaching method. The two groups of teaching effects were evaluated objectively at the end of study. Results The theoretical knowledge score of the experimental group (81.50+ 9.11) was superior to that of the control group (76.75+5.43), the difference was statistically significant (t=2.686,P=0.01).The results of clinical examination in the experimental group (87.75+4.97) was also higher than those in the control group (82.50+0.90), the difference was statistically significant (t=3.597,P<0.01).The multimedia and CBL case teaching + AT teaching method can promote mastery and use of knowledge[100.0%(36/36)], and support capacity building for self-regulated learning[97.2%(35/36)] and clinical reasoning.It also can encourage teamwork[100.0%(36/36)], inspire innovative thinking [91.6%(33/36)]. There was no significant difference between the two groups in raising learning enthusiasm and improving learning efficiency. Conclusions The application of AT teaching can improve the teaching quality of the basic experiment of surgery, and the students are more motivated and satisfied.