Abstract: Functional zoning is an essential strategy for the scientific layout and functional positioning of nature reserves, aiming to facilitate the coordinated delivery of ecosystem services. Using the Marxan With Zones model, an ecosystem service trade-off analysis was integrated into the functional zoning study of the Anhui Shengjin lake national nature reserve. Scenario simulations were conducted to derive functional zoning schemes under different conservation objectives for ecosystem services. The conclusions are as follows: (1) The Upper Lake area within the reserve and the surrounding river inflow areas hold the highest biodiversity and flood control and water storage values. The southeastern forested region exhibits relatively high values for water conservation and carbon storage, whereas food production values gradually decrease from the northwest to the southeast. Areas along the lakefront hold relatively high social and cultural values. (2) There exist varying degrees of trade-offs/synergies among different ecosystem services. Biodiversity, as a crucial ecosystem service, exhibits significant trade-offs/synergies with other services. Based on correlation coefficients, these relationships are categorized into high synergy (flood control and water storage), low synergy (water containment and social culture), and trade-off relationships (carbon solids and food production). (3) Different conservation objectives derived from the perspective of ecosystem service trade-offs lead to scenarios wherein core area sizes in the functional zoning notably increase. Furthermore, scenarios under high synergy demonstrate more comprehensive consideration for multiple ecosystem services. They exhibit higher conservation intensity for various endangered and rare bird species, overall improving trade-offs between ecosystem services and enhancing the synergy between biodiversity, flood control and water storage, and water containment. Moreover, they mitigate trade-offs with carbon solids.