Objective To explore the effect of 5S management model combined with three-dimensional digital dental and maxillary model on pain status in patients with malocclusion. Methods A total of 110 patients with malocclusion admitted to Shanghai Yangpu District Central Hospital from January to December 2024 were selected as the research subjects, and they were divided into the control group and the study group by the random number table method, with 55 patients in each group. The control group adopted 5S management model combined with plaster dental and maxillary model, and the study group adopted 5S management model combined with three-dimensional digital dental and maxillary model. The impression taking time, model data indicators and pain status were compared between the two groups. Results The single treatment time and total treatment time of the study group were shorter than those of the control group (P<0.05). There were no statistically signiffcant differences in the effective utilization rate and standardized placement rate of instruments between the two groups (P>0.05). The model loss rate of the study group after treatment was lower than that of the control group, and the model accuracy was better than that of the control group (P<0.05). The pain status in the study group was better than that in the control group (P<0.05). Conclusion For patients with malocclusion, the treatment scheme of three-dimensional digital dental and maxillary model combined with 5S management can establish digital models with high precision and low loss rate, effectively shorten the treatment cycle and relieve patients’ pain during treatment.