[4] After the handover of Taiwan from Japan to China in 1945, the CMA in Nanking appointed Chang Zichun (常子春), Wang Jingzhai and Zheng Houren (鄭厚仁) to form the preparatory committee of the CMA branch in Taiwan on 23 December 1947.

[5][6] In 1951 at the end of Chinese Civil War, the association evacuated Mainland China with the Nationalist Government to Taiwan and settled there ever since.

The mosque also holds inter-religious workshops and debates between Islam and Confucianism, Catholicism and Buddhism to promote mutual understanding with other religions.

Besides providing services for Muslims and helping to improve the welfare of Taiwan society, the association through their Overseas Affairs Commission also actively engages in cultural exchanges with Muslims in 46 countries around the world, many of which the ROC Government does not have any formal diplomatic relation with them.

[11] CMA has been sending Taiwanese Muslim students overseas to receive formal Islamic education.