The ecological value chain agricultural products in China are mainly produced by scattered farmers. Due to the lack of modern planting and breeding techniques for small-scale scattered farmers, it is difficult to obtain scale effects, and the benefit-cost ratio is generally low. Their own production, supply, and marketing integration organization can only enter the market separately, which is difficult to adapt to market needs, and often bear great market risks. In the circulation link, the agricultural product logistics management level in China is low and logistics losses are huge. This research attempts to conduct a theoretical analysis and discussion on the integration of the ecological agricultural product supply chain in China based on the enterprise theory. At the same time, we conduct an empirical analysis of the relationship between supply chain integration and performance from the perspective of logistics and build agricultural product supply chain integration with the company’s logistics capabilities as the center. We perform hypothesis model, collect data through survey methods, use quantitative analysis and path analysis methods to test the hypothesis model, explore the relationship between supply chain management and agricultural product logistics capabilities, and corporate competitiveness, to provide the empirical support for the introduction of supply chain management in the agriculture in China.