The conflict between the Catholic Church and the civilians in Chungking in 1863 is one of the most well known incidents in the Chinese Catholic history. Most researchers argue that Eugène Desflèches, the then Vicar Apostolic of Eastern Szechwan Diocese, took the Chung-Ying Temple in Chungking City by force. And his intrusion catalyzed the conflict. This article first re-examines the missionary traces of Fr. Eugène Desflèches, the characteristics of the local parish, the hierarchical structure of government officers, the relationship between Chengtu and Chungking, contentions between the Manchu and Han administrations, then suggests that Bishop Eugène Desflèches did not take Chung-Ying Temple by force. Instead, what he did was no more than a regular scrutiny, which should have authorized him to demand the return of the temple. The Manchu governors used Chung-Ying Temple as a tool to subjugate the Han administrators. As Bishop Eugène Desflèches did not take preventive measures to avoid misunderstandings, he became the scapegoat of the two contending forces. The historical records and analysis in this article present a different perspective to view the well-known incident in the Chinese Catholic history.