Changes in land use and climate and their significantly impacts on the hydrological cycle are of widespread concern to researchers and policy makers. The Soil and Water Assessment Tool (SWAT) model is used to analyze the effects of land use change and climate variability in the upper Naoli River watershed in the Sanjiang plain, northeast China. The remarkable land use changes include the decrease of woodland and wetland along with the farmland increasing. And then the rise rate has gradually diminished in recent years which should attributed to the China’s ecological environment construction project “Grain to Green” and “Convert farmland into forest and pasture” initiated in the late 1990s. Meanwhile, the climate is getting warmer and drier and the runoff variation has the same trend with precipitation and the opponent trend with temperature on the whole. Furthermore, the streamflow is affected by the combined effects of land use change and climate variability which exerts different influences in different periods. The results of this study can provide quantitative information for stakeholders and decision makers for regional water resources management and land use planning in the basin.