© 2018 by the authors. To solve the problem of unitary ecological compensation standards in river basins by scientifically clarifying the compensation for ecological protection investments and for pollution, this research divided ecological environment property relations between the upstream and downstream into three types: downstream ecological compensation for the upstream, upstream ecological compensation for the downstream and sharing the rights of the ecological environment. The various compensation standards were divided into three stages according to the location quotient and pollutant concentration. Calculation and analysis were performed for the ecological compensation of the Xiaoqing River Basin at the junction of Jinan City and Binzhou City of Shandong Province as an example. The results showed that: (1) the downstream compensations for the three stages were 2.139 billion yuan, 2.349 billion yuan and 2.489 billion yuan when only the downstream ecological compensation for the upstream was considered; (2) the compensations for the three stages were 88 million yuan, 107 million yuan, 124 million yuan when only the upstream ecological compensation for the downstream was considered; and (3) the compensations in the three stages were 2.051 billion yuan, 2.242 billion yuan, 2.365 billion yuan when ecological environment rights were shared. Under this property relation, the ecological compensation standard considering water quality and water yield and the goal of ecological environmental protection are clear and the content of compensation is complete, which is easily accepted by all parties.