Understanding the changes in hydrological process is a key subject for water resource management of a high-diversity watershed. In this paper, through an establishment of a SWAT-based model, the effects of climate change and its induced vegetation change on hydrological process were analyzed in the East River Basin. The model could well simulate the hydrological processes of the basin including surface runoff (SURQ), groundwater (GWQ), lateral flow (LATQ), total water yield (WYLD), actual evapotranspiration (ET), and groundwater recharge (PERC). Under the vegetation change induced by temperature increase, the effects of the vegetation change on hydrological process were larger than that of the temperature change. Under the vegetation change caused by the increase of temperature and precipitation, the vegetation change enhanced the effects of climate change on annual SURQ, LATQ, GWQ, WYLD, and PERC of the basin. Under spatial scale, when the temperature and precipitation changed simultaneously, the increase of precipitation could promote the increase of annual ET in sub-watersheds. Also, the annual SURQ, WYLD, GWQ and ET in western sub-watersheds were more sensitive to the cumulative changes of vegetation and climate. This work can provide useful information to decision makers in water resource management of watersheds.