Abstract: As a typical karst peak-cluster depression non-enclosed basin, the Shuangyanjing spring small watershed is 0.636 km2 in area. It is mainly recharged by precipitation through karst slocker and fissuring, and characterized by larger changing discharge with a range of 0.2～35.5 L/s. Flood peak flow calculation is inaccurate that threatening the safe operation of flood drainage engineering due to the inconsistent between surface watershed and underground watershed of karst aquifer. In order to solve the problem of lacking in long-term observation data for flood control project, this paper calculate the peak discharge as 27.5 L/s considered water-resisting layer as underground water catchment’s bound and used locate largest runoff modulus in high flow period, through karst hydrgeologic survey in the Shuangyanjing spring watershed. Then multiply the peak discharge by safety factor to get the data for wetted cross-section design. In light of the calculate results, it is suggested that to build a new retaining dam at altitude 940 m at the mouth of the Shuangyanjing valley to retain groundwater flood runoff and ease water discharge pressure in flood season.