In the development of Yangtze River Protection Project, project construction and urban operation are intertwined, so are the interest parties of the enterprise, government and society. The existing strategy selection researches can hardly reflect the synergetic relationship of all parties accurately, because the impact of the society on the construction is overlooked. Aiming at this problem, based on the evolutionary game theory and replication dynamic method, an evolutionary game model of the enterprise, government and society is constructed, and the influence of the synergetic cost and synergetic effect on the synergetic strategy selection is analyzed combined with the simulation calculation. The results show that the strategic choices of the enterprise, government and society are relevant, and only when the synergetic strategies of all parties are consistent can they remain stable; the choice of synergetic strategies of the three parties is affected by the synergetic cost and synergetic effect, the lower the synergetic cost and the stronger the synergetic effect, the greater the benefit difference between two strategies, and the easier it is for the system to evolve into a positive strategy; the increase of the synergetic effect of the enterprise and government on the society will lead to the decrease of the benefit difference of different strategic choices of the enterprise and government, which in turn will slow down the convergence speed.