The Zoige peatland is an important water conservation area in the upper reaches of the Yellow River, which plays a vital role of water storage, carbon sequestration, and ecological protection in the basin. The area of the Zoige peatland has been shrinking continuously during recent decades, which is mainly caused by the changes of its groundwater level. Here, taking a typical small peatland catchment in the upper Black River in Zoige Plateau as an example, we set up five monitoring points close to the natural channels and three away from them using the HOBO water level recorders. Analysis of the spatio temporal variation of groundwater levels in this small catchment was carried out based on the monitored groundwater level data of May-September 2017 and the meteorological data of Hongyuan Station. Results reveal that the natural channels can provide a longer effective time of water replenishment for the surrounding peat layer and they can accumulate the surface water flow faster. The change of groundwater level at the monitoring points away from the channels tended to be synchronized with the rainfall process, with the correlation coefficient between the groundwater level and rainfall reaching 0.8. The groundwater level change in the low lying land was less likely to be affected by precipitation than that in the slope land. The change of groundwater level had a lag response to the rainfall process, with the increase of rainfall intensity, the lag time gradually decreased, and the lag time of the monitoring points far away from the channels was about 18 min shorter than those close to the channels.