Objective: To explore the key variables affecting the stable operation of children basic medical insurance and put forward specific suggestions for its optimization. Methods: Vensim Software is used to establish the basic tree entry model of the flow rate of the children resident medical insurance system, and the minimal fundamental model is determined by combining the basic tree entry operation and the branch vector matrix feedback loop calculation method. Results: Key variables affecting the stable operation of basic medical insurance for children are the payment amount of medical insurance for children residents, the reimbursement standard of medical insurance for children residents, the number of insured children visiting the basic medical institutions, the quality of medical treatment for children in basic medical institutions, and the government' s resource investment in basic medical institutions. Conclusion: It is needed to reasonably set the financing standard and reimbursement standard of medical insurance for children, improve the talent incentive system in primary medical institutions, develop the quality of children's diagnosis and treatment in primary medical institutions, and rationally allocate medical resources.