The ecological construction of key eco-functional areas in Yangtze river basin impacts ecological guarantee of the whole basin, administration sets up constraint policies within the areas, leaving a higher standard in getting rid of poverty for local residents under the poverty line, which may be met by ecological compensation. This paper uses evolutionary gaming model to discuss the ecological compensation cooperation for upper- and down-stream eco-functional areas of Yangtze river basin via a strategy of protection or non-protection in up-stream and compensation or non-compensation in down-stream, and discusses the mixed stable strategy based on the above four scenarios, and presents a premium stable strategy which has been detailed in all factors of their evolutionary direction. The cooperation of precise compensation is jointly influenced by seven parameters, total cost and benefits of ecological protection, development benefits, compensation quota, punishment strength in up-stream, and compensation quota and punishment strength in down-stream, of which the total cost of ecological protection and compensation quota in up-stream and compensation quota in down-stream are key factors. This paper presents suggestion in increasing ecological compensation cooperation possibility on reducing total cost of ecological protection in up-stream and compensation quota in down-stream, raising compensation quota in up-stream and controlling punishment quota.