In food and beverage production, maintaining cleanliness is paramount, despite the emphasis placed on it, food safety incidents due to incomplete CIP still occur frequently. This study used the cleaner production of a beverage (healthy water) as a model. An intelligent CIP system employs advanced technologies such as automation, big data, and digital twin to standardize CIP-related data through modeling. Comprehensive management of the CIP process at all levels—from operators to supervisors and managers—is achieved through access control. The digital twin system ensures effective CIP execution by comparing real-time data from automated operations with standard model data. Full traceability and post-event review of CIP activities are realized through CIP order management, while big data analysis quickly identifies problem areas for continuous improvement. This approach ensures the entire CIP process is error-free, fully transparent, traceable, continuously optimized, and conducive to cleaner production.