Based on the measured daily runoff data from 1954 to 2010 at the Boluo Station of the Dongjiang River, the digital filtering method and the smoothing minimum method were used for the base flow separation. The variation characteristics of the base flow and the base flow index at Boluo station were discussed on different time scales, and the influence factors of base flow were analyzed from precipitation and human activities. It was found that the digital filtering method was more suitable than the smooth minimum method in the study area. The annual distribution of the base flow of Boluo Station increased first and then decreased, while the base flow index decreased first and then increased. The average annual base flow and base flow index at Boluo Station showed an increasing trend. The average annual base flow was 414.04 m³/s, and the average annual base flow index was 0.56. The average base flow index in both dry and partial dry years were 0.55, that in the normal year was 0.57, and that in partial wet and wet years were 0.57 and 0.55, respectively. Precipitation has an interannual impact on the base flow in Dongjiang River Basin. The change of the runoff in different months indicates that the large reservoir is a key factor in the change of the base flow in Dongjiang River Basin. The water regulation of the reservoir makes the base flow increase significantly in the dry season.