Agricultural Heritage Systems exhibit multiple functions of agricultural production, ecological protection, and invaluable cultures and landscapes. The mulberry-dyke and fish-pond system is an important agricultural heritage. The Nanxun District of Huzhou, China is currently the area with the most complete and largest mulberry dykes and fish ponds in the world. In the past thirty years, with changes in labor force distribution and consumer demand, the production function of mulberry dyke and fish ponds has been challenged, and the production landscape as the carrier of farming culture has been threatened. Studying the spatial characteristics and optimization of mulberry dykes and fish ponds is of great significance to the sustainable development of the regional economy, culture, and environment. This study analyzes the spatial and temporal pattern evolution of mulberry dyke and fish ponds in Nanxun District since 1975. Based on the evaluation of the environmental carrying capacity of fish ponds, and according to the development goals of agricultural heritage inheritance and “planting and breeding balance”, the Future Land Use Simulation model is adopted to optimize the study area. The results show the following findings: (1) From 1975 to 2019, fish ponds and construction land increased significantly, mulberry fields and paddy fields decreased significantly, the scale of mulberry dykes and fish ponds decreased significantly, and the proportion of mulberry dykes and fish ponds was seriously unbalanced; (2) The overall scale of fish-pond breeding in Nanxun District is too large, and the proportion of farming and breeding needs to be adjusted; (3) In view of economic growth, cultural inheritance, and environmental protection, this paper simulates the spatial layout of mulberry dykes and fish ponds in 2035, and divides mulberry dykes and fish ponds in Nanxun District into a display area and an industrial development area. The display area restores the traditional mulberry dykes and fish ponds to the greatest extent. The industrial development zone maximizes the economic benefits of agriculture on the basis of “balancing planting and breeding”. Overall, this study provides a reference for protecting Huzhou mulberry-dyke and fish-pond agricultural heritage, optimizing agricultural production space, balancing human–environment relationship, and promoting regional sustainable development.