Two small adjacent typical karst peak cluster-depression watersheds(Chenqi and Changchong)were chosen as the research objects, and then 26 flood processes with different magnitudes of flow were selected. The characteristics of the lag time and similarity of the surface and subsurface runoff in Chenqi watershed were compared and analyzed with those in Changchong watershed. The results show that due to the soluble rock of the depression and the threshold effect of the impervious or weakly permeable transition at the Chenqi watershed, the characteristics of the lag time and similarity between the surface and underground runoff show obvious differences. The surface runoff fluctuates more rapidly but its peak time lags behind that of the underground runoff. The flood fluctuation shape of the watershed is controlled by the surface river and it has high similarity with the flood process of the surface river. The flood process in the Changchong watershed is similar to the surface river flood process, and as the rainfall decreases, the flood shape tends to change the characteristics of the underground river runoff. The distribution of impervious rocks in the watershed reduces the aquifer's ability to regulate storage. The flood lag time in the watershed is short and the runoff responds quickly to the rainfall.