As agricultural heritage systems provide crucial ecosystem service functions, conducting functional zoning serves as a fundamental and essential approach to implementing the ecological civilization strategy and promoting targeted conservation and sustainable utilization. Taking the Mountain Spring Water Fish Farming System in Kaihua, Zhejiang, a site recognized as a China-Nationally Important Agricultural Heritage System, as a case study, this research integrates the equivalent factor method and the Self-Organizing Map neural network clustering method to evaluate ecosystem service values, identify ecosystem service clusters, and conduct ecological functional zoning. Protection and utilization strategies are subsequently proposed for each functional zone. The results show the following findings: (1) From 2005 to 2020, the total ecosystem service value of the system exhibited a fluctuating yet overall declining trend, decreasing by approximately 0.25%; (2) five ecosystem service clusters were identified, within which services generally showed synergistic relationships, while trade-offs were mainly concentrated between food provision and other ecosystem services; (3) based on these findings, the study area was divided into five functional zones—the Heritage Culture Core Zone, the Ecological Restoration and Conservation Priority Zone, the Industrial Integration and Development Zone, the Ecological–Industrial Transition and Optimization Zone, and the Multi-Value Protection and Exploration Zone. Specific protection and utilization strategies were proposed for each zone. This study provides a novel theoretical perspective and practical reference for rational ecological functional zoning, as well as the protection and sustainable use of agricultural heritage systems.