AbstractSmall hydropower projects play a significant role in supplying clean energy and promoting economic development all around the world. The calculation of a river's ecological flow, that is, not only the quantity but also the quality of flowing water, in the watershed where small hydropower projects are located play an important role in scientifically guiding the discharge of small hydropower stations in the upper reaches of the river. By combining Gini coefficient with hydrological variation diagnosis, this study provided a novel approach to test the randomness of hydrological series and assess the evenness of runoff distribution. Furthermore, this study is the first attempt to calculate ecological flow for two separate periods (flood and low‐water periods), and thus is able to better reflect annual runoff variations. In the meantime, the Tennant method was improved by introducing of monthly runoff coefficient and median substitution, and integrating four other hydrological methods (empirical method, Qp method, annual distribution method and minimum monthly average measured runoff method) into the comprehensive calculation and analysis. The above methods were applied to the ecological base flow calculation for a small hydropower project in Dongjiang River basin of China. Through comprehensive and comparative analysis, better applicability was demonstrated by the improved Tennant method and the annual distribution method. The recommended values of ecological base flow for each month were derived at the range of 407–431 m3/s during the flood period and 179–239 m3/s during the low‐water period. This study demonstrated that the method could meet the ecological flow calculation requirements for river ecosystem and provide scientific basis for the delineation of ecological flow thresholds, and thereby ensure the healthy and sustainable development of small hydropower and the healthy river aquatic ecosystem.