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Abstract Background To investigate the effect of virtual simulation systems on the teaching of inlay experiments and to guide the experimental teaching of tooth preparation. Methods Participants in their second semester of the junior year were selected to carry out the unified teaching and evaluation of dental preparation theory. The age varied from 18 to 22 years (19.96 ± 0.70) and the participants were randomly divided into four groups (n = 19) with a similar male-to-female ratio following CONSORT guidelines, including a jaw simulation model training group (Group J), a virtual simulation system training group (Group V), a jaw model training first followed by a virtual system training group (Group J-V), and a virtual system followed by a jaw model training group (Group V-J). The inlay tooth preparation assessment was performed on the extracted teeth. The data were analysed according to the assessment scores by a senior clinician. The subjective feelings of the students towards the system were evaluated using questionnaires. Results The second theoretical scores of Group V-J (63.5 ± 2.89) and Group J-V (60.5 ± 3.25) were higher than those of Group V (57.5 ± 3.13) and Group J (58.0 ± 3.67). The experimental scores of Groups J-V and V-J (62.79 ± 2.84; 64.00 ± 2.85) were higher than those of Groups V and J (56.05 ± 3.39; 55.74 ± 2.53). The questionnaire survey illustrated that most students preferred the digital virtual simulation system (perfect assessment: 91.3%, accuracy: 82.6%, satisfaction: 52.2%). Conclusion Virtual simulation training can facilitate the teaching effect of tooth preparation in inlay experiments, and the teaching mode of Group V-J was the best. Therefore, this teaching mode is to be popularised.