Objective To analyze the effect of flowable resin and glass ionomer cement filling on periodontal health indicators and filling retention in children with carious primary teeth. Methods A total of 60 children with carious primary teeth admitted to the Department of Stomatology, the People's Hospital of Xingwen County from April 2023 to April 2024 were selected as the research subjects, and they were divided into the control group and the observation group by the random number table method, with 30 children in each group. The control group was given glass ionomer cement filling for minimally invasive treatment, and the observation group was given flowable resin filling for standardized treatment. The periodontal health indicators, filling retention status and adverse reaction rate were compared between the two groups. Results There were no significant differences in PD, PLI and GI between the two groups at 12 months after treatment (P >0.05). The total shattering rate in the observation group (10.00%) was lower than that in the control group (43.33%) (P <0.05). The incidence of adverse reactions in the observation group (6.67%) was lower than that in the control group (36.67%) (P <0.05). Conclusion Both flowable resin and glass ionomer cement filling can improve periodontal health in children with carious primary teeth, but flowable resin filling can effectively reduce the filling shattering rate and incidence of adverse reactions.