Against the backdrop of medical digital transformation, West China Hospital of Sichuan University has conducted a 30-year exploration and practice of colorectal cancer data engineering. This study focuses on the integration of special disease digitization and value-based healthcare, achieving standardized management and in-depth mining of colorectal cancer diagnosis and treatment data through constructing a full-life cycle data governance system, multi-center data platform, and intelligent application scenarios (such as clinical decision support systems). The practical results show that this data engineering has formed a specialized disease database containing more than 9 500 cases of structured data, and promoted the collaborative development of the entire chain of “production–study–research–business–government”, providing a learnable digital paradigm for improving diagnostic and treatment accuracy and optimizing medical resource allocation. The study indicates that special disease digitization is a key path to achieving value-based healthcare, and its experience in data standardization and medical-engineering cross-innovation is of reference significance for other disease fields.