Climate change is one of the main factors that affect runoff changes. In the upstream of Minjiang River, the temperature increased significantly in the last 50 years, while the precipitation decreased on the contrary. In order to analyze the effect of climate change on site runoff, watershed runoff depth and evaporation, nine climate scenarios are assumed based on rainfall and temperature indicators. A SWAT model of Minjiang River is constructed, and runoff simulation is carried out with the nine scenarios. The results show that if precipitation increases or decreases 20 %, the change rate of runoff depth will increase or decrease 28–32 %; if temperature increases or decreases 2 °C, the change rate of runoff depth will decrease or increase 1–6 %; if temperature increases or decreases 2 °C, the change rate of the potential evaporation will increase or decrease 5–16 %, and the actual evaporation rate of variation will increase or decrease 1–6 %. Overall, precipitation variation has greater effect on simulated runoff than temperature variation dose. In addition, temperature variation has more obvious effect on the runoff simulation results in dry years than in wet years. The actual evaporation of watershed depends on evaporation capacity and precipitation and increases with the increasing of the potential evaporation and precipitation. The study also shows that the climate change scenarios analysis technology, combined with SWAT hydrological model, can effectively simulate the effect of climate change on runoff.