Boreal forests biomes are of great importance for regulating the hydrological cycling of global ecosystem. However, how boreal forest restoration affect the river runoff were poorly understood. In this study, two boreal forest watersheds, the upper Huma River and Ganhe River located in the Da Hinggan Mountains of Northeastern China were selected to quantify the effects of increased forest cover on runoff from 1980 to 2012 using the Budyko hypothesis associated with elasticity coefficients of runoff. The results indicated that the annual runoff existed a decreased trend associated with the rapidly increase in forest cover after the implementation of the Natural Forest Protection Project in two study watersheds. The quantitative results of the method of the Budyko hypothesis associated with elasticity coefficients of runoff showed that climate variability was the dominate driver (the relative contributions were 56.11% and 71.92% in the upper Huma River and Ganhe River watersheds, respectively) for decreasing annual runoff, while forest cover changes also played an important role for decreasing annual runoff in boreal forested watersheds in Northeastern China, which accounted for 41.20% and 23.80% of the total change of river runoff, respectively. The results of this work highlight the importance of considering the effects of increased forest biomes on streamflow and also inform our understanding of the interaction between boreal forest change and surface water resource in the study region and similar boreal forest regions across the globe.