Considering the impact of the level of fresh-keeping effort and the level of promotional effort on consumer demand in the process of selling fresh online, the consumer demand function is constructed under the common influence of the level of fresh-keeping effort and the level of promotional effort. The coordination of two-layer E-commerce of fresh agricultural products supply chain that consists of one fresh supplier and one fresh online platform is studied. According to the model, the optimal pricing of products, optimal fresh-keeping effort level, optimal promotion effort level and the profit of the supply chain members are compared with the different decision making. It is found that cooperation can improve the profits of both parties. Therefore, a compound contract coordination supply chain with “revenue sharing-cost sharing” is constructed, and the conditions for the implementation of compound contract coordination are also discussed. The results show that, the compound contract for the fresh online platform has positive impacts on the improvement of the level of fresh-keeping effort and the level of promotional effort, the effort level elasticity coefficients have different effects on the two effort level. In a certain range, with the increase of the elastic coefficient of effort level, the member income increases,when it is more than the optimal value, the increase of the elastic coefficient will cause member income damaged. Finally, a numerical example is given to illustrate the effectiveness of the hybrid contract in supply chain coordination of E-commerce of the fresh agricultural products supply chain.