To the end of the Ming dynasty, in the southeastern coast of China there appeared smuggling groups who were making a living on the sea. They normally migrated to japan illegally and worked together with the short tribe in Japan to become military force fighting against the Ming army. They even once invaded Provinces like Zhejiang and occupied fertile land there. They were what the history books cal l "Short Pirates". Among these pirates were Buddhists. This paper first reviews the earlier exchanges between China and Japan through Buddhism, then explores the Buddhist involvement in the short pirates of the Jiajing period so as to highlight the function and role played by Buddhism in the civil exchanges between China and Japan during the period concerned.