Objective To evaluate the application of flash animation video about pulpectomy of primary teeth in the prophase of clinical practice teaching. Methods Totally 60 students of 8-year-program and 5-year-program in undergraduates enrolled in 2015 who participated in the prophase of Pediatric Dentistry of Peking University School of Stomatology from May 2019 to July 2019 was randomly divided into the experimental group and the control group with 30 students in each. Flash animation video and clinical operation video were carried out respectively. The implementation effect was evaluated from the following two aspects: Students' mastery of basic knowledge and operation points, pre-clinical practice operation score. Results In terms of students' mastery of basic knowledge and operation points, the scores in the experimental group were higher than that in the control group [(4.29±0.49)vs(4.03±0.47)], especially in the access of the pulp[(4.29±0.55) vs (3.90±0.55)], root canal preparation[(4.36±0.49) vs (4.09±0.54)] and root canal filling[(4.18±0.62) vs (3.72±0.57)] (all P<0.05). In the evaluation for clinical operation, the students in the experimental group had the scored (90.67 ± 5.98) significantly higher than that of the control group (87.00 ± 6.90), (t=2.20,P=0.03). Conclusions The teaching assisted by flash animation video for pulpectomy of primary teeth is helpful to improve students' learning outcomes and support efficacy of skill training.