Abstract: Using the synergetic system model, the paper measures coordinated development level in 2000-2015 in Fujian province through constructing index system of the coordinated development of agriculture and the logistics industry. The results showed that, the development of the two-industry showed a general trend of evolution from maladjustment to gradual coordination, and the order degree of agricultural and logistics systems continued to rise alternately which promoted the coordination degree of the synergetic system to rise continuously. Lack of motivation, the degree of coordination of the two industry remains in the low-grade coordination state. From the point of view of system theory, we should start from the agriculture and logistics industry to promote the coordinated development of the linkage level.