A typical peatland watershed in the upper reaches of the Black River in the Zoige Basin in the Source Region of the Yellow River is taken as the research object. The groundwater level monitoring data, meteorological data, and unmanned aerial vehicle aerial survey topographic data in 2018-2022 were used to statistically analyze the spatiotemporal changes of the groundwater level in the peatland watershed, and the section depth and discharge process of the channel outlet in the watershed were calculated. The results show that precipitation is the dominant factor of groundwater level change in the peatland watershed, and the changing trend of groundwater level is consistent with that of precipitation, which increases with the increase of the ratio of precipitation to evaporation. The groundwater level in the middle reaches of the small basin fluctuates more violently than that in the upper reaches. The average groundwater level in the upper reaches is higher than that in the middle reaches, and the water storage capacity of the peat wetland in the middle portion is decreasing. Based on the hydraulic method and the monitoring data of groundwater level, the empirical relationship formula between water depth and discharge in the channel sections of the peatland watershed is obtained, which can be used to calculate the daily discharge process line.