Abstract: The Zhaidi karst underground river system is located in Guangxi of southwest China and is a typical karst spring catchment with a mean annual discharge of around 1.62 m3/s. The catchment area is about 31.05 km2, with altitudes ranging from 190 m to 820 m a.s.l, and is developed mainly in the Devonian limestones with the landform type of karst peak-cluster depression. Precipitation mainly takes place in spring and summer and mean annual precipitation recorded from 1971 to 2000 is about 1,601.1 mm. The Zhaidi karst underground river system is characterized by extremely anisotropic fractured carbonate rocks and well interconnected karst conduits. There are eight karst underground river sub-systems and many sky-windows, pools and sinkholes. According to tracer tests, these eight subsystems are also well connected each other, where the groundwater runs from the sinkhole G37 through the karst conduits toward the outlet G47. Although numerical technique is a powerful tool for evaluating karst water resources, but it is difficult to accurately depict the pipe flow in the karst conduits in the model due to its anisotropic property. In this paper, the conduit flow of the Zhaidi karst basin was studied, by using Drain module and River module in MODFLOW to simulate the karst conduit, for which the applicability of the modules was examined by the data derived from three observation boreholes respectively situated in the upstream, midstream and downstream of the basin. To observe the groundwater level fluctuation and to obtain the time series data, two boreholes (ZK7 and ZK8) were drilled on the conduit with intention. From upstream to downstream, the distances between sinkhole G37 and borehole ZK7, borehole ZK7 and ZK8, borehole ZK8 to outlet G47 are 1,400 m, 900 m, 140 m, respectively. In addition, the outlet G47 was equipped with a rectangle sharp-crested weir with a level logger installed. The results showed that there was a sudden change of the water table contour near conduit and the water level variation trend was simulated, which meant both of method could conform to the actual conduit features. At last, the principle of two simulation methods were analyzed which showed karst conduit in Drain module only played a drainage role without exchanging water, while in River module it could exchange water with aquifer. It can be concluded that River module is better that Drain module to simulate karst conduit flow.