River runoff is an important form of water resources, and baseflow is a vital part of the runoff. It is of great significance to study the change of baseflow and its influencing factors to master the change of water resources in the basin. Based on the daily flow data of Qujiang Basin from 2007 to 2018, the applicability of nine different baseflow separation methods and the variation characteristics of baseflow were analyzed. The results showed that: (1) There were great differences among different methods, and the separation results of time step method and sliding minimum method were higher than others. The variance and coefficient of variation of F4 filtering method were 0.038 and 0.138, indicating that the separation of this method was more stable and less discrete, and had the best applicability in the Qujiang Basin. (2) The multi-year average baseflow index of the basin was 31.5%, and there were both summer and autumn flood seasons in the year, the multi-year average monthly precipitation, runoff and baseflow had the same variation trend, and the peak time of runoff and baseflow in the basin showed a lag compared with precipitation. (3) Wavelet coherence analysis showed that both precipitation and baseflow series in the basin had a 10~14 months variation cycle and changed in the same direction, the baseflow lagged behind the precipitation series in time and frequency, and the baseflow had a time delay in response to climate change. When the baseflow lagged 8~10 months behind the climatic index of the same period, the correlation between the two was significantly increased. The research results are helpful to improve the understanding of the change of baseflow in the Qujiang basin and provide a scientific basis for the management and regulation of water resources in the basin.