Background: The medical cost reimbursement function of medical insurance can reduce the medical burden of individuals and thus improve their medical service utilization level. This study aimed to explore the impact of different cross-regional reimbursement types of medical insurance (instant reimbursement and manual reimbursement) on the hospitalization costs incurred by the floating population. Methods: The data used in this study was from the 2018 China Migrants Dynamic Survey (CMDS) conducted by the National Health Commission of China. The multiple linear regression model and Propensity Score Matching method (PSM) were used to analyze the impact of instant and manual reimbursement on hospitalization costs. Results: (1) Instant reimbursement and manual reimbursement could significantly reduce the floating population’s out-of-pocket proportion of hospitalization costs by 33.2% and 26.9%, respectively; (2) the average proportion and amounts of out-of-pocket hospital costs of instant reimbursement for the floating population were lower than those of manual reimbursement by 6.35% and 19.6%, respectively, and this impact would gradually increase as the flow distance expanded; (3) there was no significant impact of instant reimbursement on the total hospitalization costs relative to manual reimbursement. Conclusions: Our study suggests that instant reimbursement can effectively reduce the out-of-pocket medical burden of the floating population at the individual level, but it will not have an obvious impact on the total hospitalization costs at the social level.