Objective: The paper analyzes the intrinsic mechanisms of score-fee adjustment in Shenzhen City’s DIP disease catalog from 2023 to 2025, constructing a causal chain from catalog adjustment, hospital behavior response to fund operation outcomes, and revealing the deep transition logic from “cost-management tool” to “value-based purchasing”. Methods: Three annual DIP disease catalogs from Shenzhen City were analyzed with a focus on benchmark score and average fee changes. Combined with actual DIP settlement data from a tertiary hospital in Shenzhen City, whose DIP unit score price is 12.12 yuan in 2024 and 11.48 yuan in 2025, we employed paired comparative analysis, revenue and expenditure impact assessment, and causal path analysis to systematically validate the transmission effects of catalog adjustments on hospital behavior based on the description of the evolution pattern. Results: Among 4773 comparable disease categories between 2024 and 2025, 61.2% experienced score reductions with a median decrease of 1.75%. Average costs for core diseases fell 9.3% (from 18963 to 17198 yuan), while median benchmark scores decreased 4.7% (from 796.92 to 759.38). Conclusion: The score-fee adjustment mechanism in Shenzhen City’s DIP catalog reflects an institutional transition from “broad coverage and aggregate control” to “precision allocation and value-based purchasing”. The compounding effects of continuous score declines and fixed unit prices have triggered structural changes in hospitals. Dynamic score adjustment mechanisms based on medical service value assessment are recommended to establish a closed-loop feedback system comprising data monitoring, effect evaluation, and parameter optimization, achievingthe dual goals of medical insurance fund efficiency and sustainable hospital operations.