This paper analyses the differences on China’s agriculture export to Japan and Korea of the amount, structure and trade barriers from the perspective of China-Japan-Korea FTA construction. It finds that China’s agricultural export to Japan is much larger than that to South Korea, and export growth is more stable. China’s export of agricultural products to Japan is more concentrated and stable, which mainly focuses on aquatic products and vegetables, while the structure and proportion of China-to-Korea agriculture goods changes. As to trade barriers, South Korea adopts a much higher level of tariff rates while Japan requires higher standards of technical barriers and tax quotas. In this view, in order to promote China’s agriculture export, there are needs to establish unified agricultural safety standards and inspection and quarantine procedures between China, Japan and Korea. Furthermore, technical exchanges and cooperation must be strengthened under the construction of China-Japan- Korea FTA.