Objective To explore the effect of systematic nursing on mental health status in children with congenital syndactyly undergoing ffap reconstruction. Methods A total of 50 children with congenital syndactyly who underwent ffap reconstruction at the Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College of HUST from April 2022 to April 2025 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 25 children in each group. The control group received conventional nursing, and the observation group received systematic nursing. The mental health status, treatment compliance, quality of life, complications rate and nursing satisfaction were compared between the two groups. Results The scores of mental health status in the observation group after nursing were higher than those in the control group (P<0.05). The treatment compliance rate of the observation group (96.00%) was higher than that of the control group (72.00%) (P<0.05). The score of SS-QOL in the observation group after nursing was higher than that in the control group (P<0.05). The incidence of complications in the observation group (8.00%) was lower than that in the control group (12.00%), but the difference was not statistically signiffcant (P>0.05). The nursing satisfaction rate of the observation group (100.00%) was higher than that of the control group (84.00%) (P<0.05). Conclusion The application of systematic nursing during the perioperative period of flap reconstruction for children with congenital syndactyly can effectively prevent complications, improve children's mental health status, enhance their quality of life and treatment compliance, and increase the satisfaction of children's families with nursing services. It is worthy of clinical application.