Mouly was a member of the Congregation of the Mission founded by St. Vincent de Paul, better known as Vincentians. At the age of 26, he left his native France for China, where his responsibilities increased steadily. By 1836 he had become superior of the French Vincentians in northern China. In 1842 he was ordained the first bishop of the newly created vicariate apostolic of Mongolia. Five years later the Holy See added to this task that of administrator apostolic of the diocese of Peking (Beijing). Finally, in 1856, when this diocese was abrogated and divided into three vicariates apostolic, Mouly became the first vicar apostolic of North Chihli, with residence in Peking.
Historians of modern China often fault Mouly for excessive displays of Gallic nationalism and heavy reliance on the French protectorate over Catholic missions. On the other hand, he also played a key role in expanding and organizing the Catholic Church in China.