The invention discloses a drainage basin water environment quality ecological compensation method, which comprises the following steps of (1) obtaining drainage basin provincial-controlled river monitoring cross section water quality monitoring data; (2) performing quarter checking on the provincial-controlled cross section water environment quality improvement condition in each district division city; performing business accounting in each quarter according to a formula; issuing eco-compensation fund; (3) performing one-time added bonus on the single provincial-controlled cross section stably reaching the ground surface water environment district division or excellent water quality control requirements; performing business accounting in each year; issuing the next one-time added bonus; performing annual continuous penalty on the single provincial-controlled cross section incapable of stably eliminating five kinds of water bodies; accounting compensation fund in each year according to the method. The step is simple; the method is convenient; the practicability is high.