Objective: To explore the application effects of glass ionomer cement and photosensitive composite resin in the filling treatment of dental caries in primary molars. Methods: From April 2022 to January 2024, 88 cases of children with primary dental caries treated in our hospital were selected as the research subjects. According to the random number table method, the 88 children were divided into the cement group and the resin group, with 44 cases in each group. The cement group were treated with glass ionomer cement filling, while the resin group were treated with photosensitive composite resin filling. The recent and follow-up efficacy of both groups were recorded. Results: After 3 months of treatment, the excellent and good rate of the cement group were 97.73%, which were higher than the 86.36% of the resin group, and the difference were statistically significant (P<0.05). After 3 months of treatment, the gingival bleeding index and plaque index of the two groups were lower than before treatment. The cement group were also lower than the resin group after 3 months of treatment, and the difference were statistically significant (P<0.05). During 12-month follow-up, the filling integrity rate and secondary caries incidence rate of the cement group were 97.73% and 0.00%, respectively, while those of the resin group were 84.09% and 11.36%, respectively. The difference between the two groups were statistically significant (P<0.05). During 12-month follow-up, the incidence of complications such as pulpitis, filling loss, and tooth sensitivity in the cement group were 4.55%, while in the resin group it were 18.18%. The cement group were significantly lower than the resin group (P<0.05). Conclusion: Compares with photosensitive composite resin, the application of glass ionomer cement in the filling treatment of dental caries in primary molars can improve the short-term treatment effect, reduce gingival bleeding index and plaque index, lower the incidence of follow-up secondary caries and complications, and promote the improvement of filling integrity rate in children.