The Sanjiang Plain is one of China's largest and most vital grain-producing regions, with agricultural intensification being one of its most representative characteristics. However, the impacts of this agricultural intensification on local freshwater organisms remain poorly understood. There is an urgent need to analyze the driving weights of natural biogeographic and anthropogenic factors across multiple dimensions, in order to establish a balance point for biodiversity conservation and sustainable agricultural development . Therefore, we examined the relative importance of land use change compared to geographic climate, local environmental factors, and spatial variables on fish community β-diversity, considering three dimensions: taxonomic, functional, and phylogenetic . The results demonstrate a significant ecological information correlation among the three dimensions of β-diversity of fish in the Hulan River, with the turnover component being predominant across all dimensions (89.04 % in taxonomy, 79.40 % in functionality, 83.59 % in phylogenetic). This suggests that species-level management within multiple small spatial scales within the basin can effectively conserve the majority of fish species, functional traits, and lineages . Land use exerts the most significant influence through environmental filtering (pure contribution of variance is 0.061–0.110). Woodland area, turbidity , and water depth are the primary environmental drivers. Strong land-use gradients may have shaped this β-diversity pattern. Fish communities exhibit high sensitivity to alterations in the extent of woodland or cropland. Implementing land use planning with gradient characteristics within the basin, particularly emphasizing the gradient change pattern of woodland, is crucial for maintaining the high β-diversity of fish in the Hulan River. • The fish β-diversity across the three dimensions in the Hulan River carries similar ecological information, with all dimensions being turnover dominated. • Woodland area is the most crucial driver, followed by turbidity and water depth. Fish β-diversity is highly sensitive to changes in woodland and cropland area. • Gradient-based land use planning , especially for woodland/cropland, is vital for maintaining high fish β-diversity.