The Nanjing Church Incident occurred in 1616. It was initiated by an official surnamed Shen in Nanjing. This official held a post in Nanjing in 1615. At that time, Catholic churches had been built in Nanjing, and Catholicism had witnessed much development there. In 1616, he wrote several letters to the emperor, severely criticizing the creeds and believers of Catholicism. He thought that the Catholics did not respect the emperor and Chinese culture. Being a Confucian, he completely denied Catholicism by listing various reasons and citing a series of evidence. He even claimed that the Catholic calendar had harmed the moral order of Chinese.

His first two attempts failed. Then he allied with a favorite of the emperor and several high-ranking officials to attack Catholicism. This time he succeeded. Some missionaries were arrested and a series of misdeeds of Catholicism were officially denounced. Other missionaries had to return to the south. The churches they built were destroyed and some graves were damaged. This incident lasted for three years before Catholicism resumed its activities in 1621 when Shen was dismissed from his post.