In order to explore the effect of check dams on runoff process and elucidate the mechanismunderlying erosion reduction, we chose a representative basin in the first sub-region of the hilly and gully loess region with well-established check dam system as the research subject. Firstly, we analyzed the influence of check dams on runoff coefficient, sediment transport modulus and basin lag time. The result shows that the runoff coefficient of Jiuyuangou,Wangmaogou and Xiangtagou was reduced by 29.43%, 34.63% and 16.78% and the sediment runoff modulus was decreased by 28.09%, 67.75% and 27.75%, respectively, compared with Peijiamao, Lijiazhai and Tuanyuangou which were not governed. The basin lag time of Wangmaogou was 117 min, almost three times longer than that of Lijiazhai. Secondly, we analyzed the effects of the check dam siltation on flow discharging capacity through establishing the unit discharge concept. We defined the flow of cross section of any channel under 1 m water level as the specific rate of flow. A Chezy formula was used to calculate the flow through the channel unit. The results illustrated that the flow rate of natural channel unit was 41.82 m3 / s, while the flow rate of check dam was 17.13 m3 / s. With the dam siltation, deposition reduced the flow capacity of the channel, and the unit flow rate of channel was reduced to 40% of the original. Finally, we defined three kinds of the river nodes which are reach junction (river junction), reach barriers node (check dam) and reach feature transform node (the transition point of natural channel to siltation channel), and divided the reach barriers node into three sub.categories which are strong connectivity node (spillway), weak connectivity node (shaft and horizontal pipes) and disconnected node (check dam without water facilities) based on the category of water release works. According to the unit flow, we assigned weight to each kind of node, constructed the river tree graph of Wangmaogou watershed by graph theory, and calculated the weight value of the whole basin (0.21). By fitting the measured peak flow, we found that there is a good correlation between the weight value and peak flow. The results are of significance to analyzing the influence of check dams and other measures of soil and water conservation on hydrological process of watershed.