A method has been developed based on the Soil and Water Assessment Tool (SWAT) to quantitatively evaluate the water conservation function of forests and its multi-time scale characteristics in a discontinuous forest watershed. Using this method, we have divided hydrological response units (HRU) based on the spatial distribution of forests, and derived a formula to quantify the water conservation in discontinuous forest watershed based on the water balance method. Here we take the Jinjiang River Basin in southeast coastal China as an example. We constructed SWAT model under land use conditions in 2006 and analyzed the temporal variation of forest water conservation in the study river basin under precipitation conditions from 2002 to 2010. The results show that (1) the SWAT model of the study area is of high accuracy, and the hydrological response unit can accurately reflect the distribution of forest patches when the area threshold is zero. The model provides a new method for evaluation of forest water conservation function in the discontinuous forest watershed using a distributed hydrological model. (2) The annual conservation of forest water in the Jinjiang River Basin was 271.41-565.25 mm. The annual conservation function of forest water is relatively stable, and there was no runoff regulation between consecutive years. The monthly conservation ranged from -29.15 mm to 154.59 mm, which is positive for most months of the year. The forest water conservation was positive in extreme precipitation period, and negative in extremely dry period. This demonstrates the function of forest water conservation in retaining rainwater in wet periods to decrease flood in the river and supplying water in dry periods to supplement the flow at the daily scale was more effective than that at the monthly scale.