Objective To explore the effect of modified high-strength glass ionomer atraumatic restorative treatment on periodontal health status in children with deciduous tooth caries. Methods A total of 144 children with deciduous tooth caries admitted to the Department of Stomatology, the Friendship Hospital of Ili Kazak Autonomous Prefecture from July 2023 to July 2024 were selected, and they were divided into the control group and the study group by the random number table method, with 72 children in each group. The control group was given composite resin restoration, and the study group was given modified high-strength glass ionomer atraumatic restorative treatment. The clinical efficacy, filling effect, aesthetic effect, patient cooperation and periodontal health status were compared between the two groups. Results The total effective rate of the study group (100.00%) was higher than that of the control group (94.44%) (P<0.05). The imaging effect score and tooth function score of the study group after treatment were better than those of the control group (P<0.05). The aesthetic effect score of the study group after treatment was higher than that of the control group (P <0.05). The patient cooperation rate of the study group was 95.83%, which was higher than 80.56% of the control group (P <0.05). The scores of PLI and GI in the study group after treatment were lower than those in the control group (P <0.05). There was no statistically significant difference in PD between the two groups (P >0.05). Conclusion The modified high-strength glass ionomer atraumatic restorative treatment technology can provide better filling effect and aesthetic effect for patients, which is helpful in improving patient cooperation. At the same time, it can improve periodontal health, thus effectively ensuring the overall treatment efficiency.