A small watershed, the catchment of the Yangshudang reservoir, in Zhanghe irrigation area located in Hubei Province and the catch - ment of the Qingshitan reservoir in Guangxi Zhuang Autonomous Region were selected as the study area. And the digital filter technology was used to the baseflow separation for the runoff based on the daily inflow runoff of the Yangshudang reservoir and the monthly inflow runoff of the Qingshitan reservoir. The results show that the baseflow index Fr increase along with the growing of the time scale. The baseflow index Fr of daily runoff is smaller than that of ten days and monthly runoff in catchment of the Yangshudang reservoir, and the baseflow index Fr of monthly runoff is smaller than that of seasonal and annual runoff in the Qingshitan reservoir. Also baseflow index Fr of inflow runoff in the Yangshudang reservoir, a non-karst area is smaller than that in the Qingshitan reservoir.