Fuxian Lake, China"s largest deep freshwater lake in terms of water storage capacity, has seen its water level decline since 2010 due to reduced inflow and other reasons, affecting the natural reproduction of its indigenous fish species. To protect the rare fish resources and biodiversity of Fuxian Lake, and to ensure the healthy and sustainable development of its ecosystem, it is imperative to determine a suitable ecological water level that promotes the habitat protection and restoration of its endemic fish species. This study focused on the endemic fish, Anabarilius grahami, of Fuxian Lake, taking it as the target species for analysis. Based on the habitat requirements of Anabarilius grahami during its growth period, three crucial habitat factors were identified: water temperature, flow velocity, and dissolved oxygen (DO). Given Fuxian Lake’s characteristic as a deep lake, a three-dimensional hydrodynamic and water quality model was constructed using the Environmental Fluid Dynamics Code (EFDC). The Vertical Cumulative Weighted Usable Area (VCWUA) tailored for deep lakes was proposed, leveraging the habitat simulation method to calculate the suitable ecological water level for Fuxian Lake and assess its feasibility. The study yielded several key findings: ①The spatial distribution characteristics of the Suitability Index(SI) for the three key habitat factors — water temperature, flow velocity, and DO — exhibit differences. The SI for water temperature and flow velocity show minimal variation at different depths and have little impact on the comprehensive HSI. However, the SI for DO decreases significantly when the water depth exceeds 15 meters, which is the main factor affecting the vertical distribution of suitable habitat space. ②The variation of the Weighted Usable Area (WUA) in the living space (0-20m underwater range) of Anabarilius grahami is the same under different water level schemes. As the water depth increases, the WUA first increases and then decreases, peaking at a depth of 15 meters underwater. ③By analyzing the relationship between the water level of Fuxian Lake and the VCWUA of Anabarilius grahami, it is observed that the VCWUA increases initially and then decreases as the water level rises. The target value of the suitable ecological water level corresponding to the maximum value of the curve is 1722.29 m. Considering predictions of water level changes driven by climate change and human activities, as well as the scale of water diversion projects implemented in the Fuxian Lake basin, it is deemed achievable to attain this target water level.