Numerous papers have utilized distributed hydrological models to assess the hydrological effects of land use changes. However, can these models reflect actual land use changes? This study focuses on the effect of calculation unit division in distributed hydrological models on the analysis of hydrological effects of land use change. The Soil and Water Assessment Tool (SWAT) model is tested here, using the Dongjiang headwater region in southern China as the study area. Thirteen calculation unit division schemes are developed to analyze the effects of land use generalization caused by calculation unit division on runoff and sediment load simulations by SWAT. Two indices, including Land Use Identification Accuracy (LUIA) and Land Use Change Identification Accuracy (LUCIA) are employed to quantify the model’s precision in describing land use and changes under various scenarios. In addition, this study examines how differences in land use descriptions, resulting from calculation unit division, influence the hydrological effect of land use changes in the SWAT model. The findings indicate that: (1) Calculation unit division leads to the generalization of land uses identified by the SWAT model. As the sub-watershed Drainage Area Threshold (DAT) increases, the small land use types tend to aggregate into the larger land use types. (2) Land use generalization, resulting from calculation unit division, significantly affects runoff and sediment load simulations. An increase in DAT induces a significant rise in simulated runoff and sediment load (P<0.001). (3) Calculation unit division substantially impacts the model’s description of land use. LUIA and LUCIA show a significant downward trend as DAT increases. (4) Calculation unit division significantly alters the analysis results of hydrological effects of land use changes. Different calculation unit division schemes yield different analysis results of hydrological effects of land use changes. These results demonstrate that the division of calculation units in the SWAT model leads to land use generalization, which impacts the model’s description of land use changes and subsequently affects the assessment of the hydrological effects of land use changes. The research results imply that when analyzing the hydrological effects of land use change, a more refined calculation unit division scheme should be adopted as far as possible to improve the accuracy of model’s description of land use change and reduce the uncertainty of model simulation results.