During the reform of DRG/DIP payment methods, the special case negotiation mechanism plays an important role in ensuring the scientific and fairness of the reform, and guiding value-based healthcare. The special case negotiation mechanism embodies the scientific idea of special treatment for special situations and specific analysis of specific problems based on facts, which is a necessary measure to ensure the smooth progress of DRG/DIP payment reform. The practice in Dongying City has proved that to make good use of the special case negotiation mechanism, its principles must be clarified, its necessity must be clarified, and the use of the special case negotiation mechanism should be regarded as a part of implementing DIP payment reform. In practice, it is necessary to attach great importance to the openness and transparency during the entire process, strictly follow the evaluation standards from a detailed perspective, promote closed-loop management with the use of data analysis, adhere to the essential principle of “ensuring basic medical insurance” as the direction, and continuously improve and make good use of the special case negotiation mechanism in the DIP payment reform.