Abstract: Based on analyzing the present situation of modern agriculture in Fujian, the competitiveness of modern agriculture in Fujian was analyzed from five aspects including Yield Comparative Advantage Index, Scale Comparative Advantage Index, Integrated Comparative Advantage Index, domestic market share and Revealed Comparative Advantage Index. The results showed that the overall competitiveness of agriculture in Fujian was strong at present, but the competitiveness mainly represented in resource superiority and there were more primary agricultural products. Based on the analysis, the countermeasures were put forward including optimizing the industrial structure to highlight the characteristics of resources, improving the scientific research mechanism to develop the work of science and technology supporting agriculture, taking advantage of Fujian and Taiwan to accelerate the west-strait construction and promote the communication and development of characteristic agricultural products between Fujian and Taiwan.