In recent decades, large-scale vegetation restoration has been carried out in the middle reaches of the Yellow River, which is a significant factor leading to the reduction of runoff in many watersheds. Since 1988, the source area of the Fenhe has continuously carried out three phases of comprehensive soil and water conservation management, and the forest vegetation coverage in this area has significantly increased. However, the runoff in the Fenhe source area has shown an opposite increasing trend. The impact mechanism of changing environment on runoff and its components in the area is not yet clear. Beishihe is an important tributary of the Fenhe source area, and the runoff change in this watershed is mainly caused by the impacts of vegetation restoration and climate change. Therefore, this study selected the Beishihe watershed as the study area, and used 9 numerical simulation methods to separate the baseflow from 1962 to 2018. The trend of runoff, surface runoff and baseflow and their mutation years were analyzed using the Mann Kendall test and cumulative anomaly method. The impacts of vegetation restoration and climate change on runoff and its components were evaluated by the double cumulative curve method, regression analysis method, and elastic coefficient method. Results show that: (1) among the nine numerical simulation methods, the Lyne-Hollick filtering method had relatively higher estimation accuracy, and its daily baseflow process line could better reflect the hysteresis and stability of the baseflow. Thus, it was more suitable for baseflow estimation in the study area. (2) The average annual runoff depth, surface runoff depth, baseflow depth, and baseflow index of the watershed were 181.2 mm, 67.4 mm, 113.8 mm, and 0.68, respectively, which indicated the baseflow was the main component of runoff. The annual runoff and annual surface runoff showed an insignificantly increasing trend, while the annual baseflow showed a significantly increasing trend. The increase of baseflow was the main direct cause of runoff change. In addition, the results of mutation test showed that the abrupt changes in annual runoff and its components all occurred around 1994. (3) The precipitation change led to an increase in runoff, surface runoff, and baseflow, which played a key role on runoff change (the contribution rate was 78.1%-79.4%). Vegetation restoration led to an increase in runoff and baseflow, as well as a decrease in surface runoff. The main reason is that vegetation restoration could promote precipitation infiltration, thereby reducing surface runoff. At the same time, the soil and landform conditions of the Beishihe watershed made the increased precipitation infiltration more likely to form baseflow. The increase in baseflow caused by vegetation restoration exceeded the decrease in surface runoff caused by vegetation restoration, ultimately increasing the total amount of runoff. The study can provide scientific basis for the reasonable restoration of vegetation and sustainable utilization of water resources in the source area of the Fenhe.