The characteristics and reform practice of special cases under DIP payment were analyzed, and policy optimization measures were discussed. A total of 2926 special cases in 2022 was selected from the sample cities, and quantile regression analysis method was used to explore the influencing factors of their costs. The results showed that the characteristics of the special cases were mainly tertiary hospitals, senile patients, long hospitalization, multi-operation or multi-discipline treatment, and conservative group diseases. Multiple factors such as institution level, length of hospitalization, negotiation type, transfer of department, discharge method, and disease attributes jointly affect the hospitalization costs of special cases. The special case negotiation promotes the scientificity and accuracy of payment through reasonable compensation for special cases, and supporting mechanism such as negotiation and supervision assessment promotes the refined management of medical insurance. It is suggested that the conditions for the application of special cases should be reasonably determined, the adjustment mechanism for core elements should be improved, supporting policies should be launched, and the combination of reform should be implemented.