As a well-built, distributed hydrological model, the Soil and Water Assessment Tool (SWAT) has rarely been evaluated at small spatial and short temporal scales. This study evaluated crop growth (specifically, the leaf area index and shoot dry matter) and daily evapotranspiration at the hydrological response unit (HRU) scale, and SWAT2009 was modified to accurately simulate crop growth processes and major hydrological processes. The parameters of the modified SWAT2009 model were calibrated using data on maize for seed from 5 HRUs and validated using data from 7 HRUs. The results show that daily evapotranspiration, shoot dry matter and leaf area index estimates from the modified SWAT2009 model were satisfactory at the HRU level, and the RMSE values associated with daily evapotranspiration, shoot dry matter, and leaf area index were reduced by 17.0%, 1.6%, and 71.2%, compared with SWAT2009. Thus, the influences of various optimal management practices on the hydrology of agricultural watersheds can be effectively assessed using the modified model.