Abstract: Background Quantitative analysis on the effects of climate variability and human activities on runoff is one of the keys to inquiring about runoff change mechanism and control of soil erosion. Minjiang River is the largest river in Fujian Province,and the change of water resources has important influence on social economy and ecological environment. In recent years, many researches focused on the change characteristics of runoff, precipitation and temperature in Minjiang River Basin. However, little studies have reported on the change characteristics of potential evaporation, and the relative effects of climate variability and human activities on runoff. Methods The observed monthly river discharge of 4 hydrological stations and monthly meteorological data (precipitation, temperature, wind, sunshine hours, and relative humidity) of 23 meteorological stations for the period 1960 2010 were collected. Characteristics of the variation of hydro-climatic changes over the last 51 years were analyzed based on the TFPW-MK, and the relative effects of climate variability and human activities on runoff were investigated based on an empirical discriminant method and climate elasticity method. Results Firstly, runoff and precipitation of the Minjiang River were on the rise in general while potential evaporation was declining and had a sudden change in the early 1970s. Secondly, relative effect of climate variability was greater than that of human activities in Minjiang River Basin and three sub-basins under different decades relative to 1960s, except in the beginning of 21st century in Jianxi River sub-basin and Shaxi River sub-basin, in which the contributions of human activities accounted for 60% and 52% of the changes in streamflow, respectively. Additionally, the contribution of the climate variability on the runoff in Minjiang River Basin and Futunxi River sub-basin was the largest in the 21st Century, accounting for 86% and 89% of runoff changes respectively, and the contribution of the climate variability in Jianxi River sub-basin and Shaxi River sub-basin was the largest in 1990s, accounting for 86% and 89%, respectively. Conclusions In general, the results from the empirical discriminant method and climate elasticity method were the same on the whole, climate variability leaded to an increased streamflow while human activities always resulted in a decrease of streamflow. The increase of precipitation and decrease of potential evaporation were the major reasons for the increase of runoff. Moreover, the relative effects of climate variability and human activities varied among sub-basins, and the differences in the internal climate and human activities were the main reasons. The impact of climate variability on runoff was the most significant in the Minjiang main stream and three sub-basins in 1990s; the impact of human activities on runoff was the most significant in the Minjiang main stream and Futunxi River sub-basin in 1990s and in Jianxi River sub- basin and Shaxi River sub-basin in 1980s and the beginning of the 21st century, respectively.