Based on the farmland distribution maps of Naolihe River Basin in 1990 and 2013, the influences of paddy farmland and cultivation activity on temporal and spatial variation of water cycle process were analyzed quantitatively, combining with TOPMODEL model based on LBM method. Results showed that TOPMODEL model based on LBM method could simulate well the rainfall runoff process of Naolihe River Basin, and it had a high applicability on the investigated river basin. The area of forest land, grassland and construction land was not changed much, which contributed little to the change of land structure, while unused farmland and dry farmland were partly converted to paddy farmland, contributing obviously to the change of land structure. The presence of paddy farmland resulted in the increase of total evapotranspiration, decrease of the water deficit in root zone, decrease of water deficit in the unsaturated zone, decrease of surface water, and increase of underground water from May to October. Evapotranspiration was increased by 8.9%, water deficit in the root area was decreased by 10.5%, and surface water was decreased by 43%. Paddy farmland showed different effects on hydrological variables when rice was in different growth stages. It had great influence on evapotranspiration, water deficit in root zone and water deficit in unsaturated zone when rice was in tillering stage. The influence of paddy farmland irrigation on different water cycle processes was diminished in the sequence of SBAR, RZ, E, water quantity in inlet of root zone, water quantity in outlet of root zone, and RG, among which the differences of water quantity between irrigation and non-irrigation were almost the same for the inlet and outlet of root zone.