Guangdong trade with Japan started in the middle period of Ming Dynasty. During the late Ming to the early Qing，Guangdong merchant ships began to increase，maintaining a large scale，due to the Japanese shogunate’s encouragement. However，some merchants gradually began to choose Zhejiang ports to Japan for the impact of geographic and seasonal factors，specially for the foreign policy of the Qing and Japanese government. Until the late Kangxi，the trade of Guangdong merchants directly to Japan completely interrupted. The article thus explains that we should pay attention to the discussion of the impact of policies and systems in the Sion-Japanese trade.