Objective To explore the effect of bracketless invisible appliance on periodontal indicators and inflammatory factor levels in gingival crevicular fluid of children undergoing orthodontics treatment. Methods A total of 86 children who received orthodontics treatment in Yancheng Stomatological Hospital from January 2023 to January 2024 were selected, and they were divided into the control group and the observation group by computer-generated randomization, with 43 children in each group. The control group was treated with fixed appliance, and the observation group was treated with bracketless invisible appliance. The periodontal indicators, inflammatory factor levels in gingival crevicular fluid, and complication rate were compared between the two groups. Results There were no statistically significant differences in GCF and PD between the two groups after orthodontics treatment (P >0.05). The PLI and SBI of the observation group after orthodontics treatment were lower than those of the control group (P <0.05). The levels of MMP-8 and sICAM-1 in the observation group after orthodontics treatment were lower than those of the control group (P <0.05). The incidence of complications in the observation group (6.98%) was lower than that in the control group (23.26%) (P <0.05). Conclusion The application of bracketless invisible appliance in children undergoing orthodontics treatment can effectively improve periodontal indicators, reduce the levels of inflammatory factors in gingival crevicular fluid, and help to reduce complications, which is worthy of clinical application.