明代承天能仁寺恢复重元寺的旧名。寺内这时开始修造了高大的万佛阁，里面有佛像万尊；经、钟二楼和无量、观音二殿也得到了重修，同时又增修了盘沟殿、末理大殿以及旃檀林、桂花园。承天阁巨大无比，万佛楼众佛林立。观其栋宇之宏壮，构缔之精宻，庄严丹碧之华缛而明丽，在他方盖不多，而于呉则仅有也。
明崇祯十一年（公元1638年）重元寺浚井，从井中掘得的宋末元初人郑思肖（所南）所著的《心史》一书，该书以诗以文记宋亡时杂事，被视为民族心灵历史的象征。

Edward Nengren to restore the Ming Dynasty temple re-yuan Temple of the old name. Temple then started to build a tall Foge million, there are 10,000 Buddhist statues; through, 10 minutes and the second floor of the immeasurable, Kwun Yam Temple II have been renovated, at the same time, the amendment set groove Hall, the end of the hall and Zhan Tan Li Lin, Guangxi Garden. Edward Pavilion enormous, floor to poke many Buddhist people. Its view of the Hong Zhuang-Dong Yu, the association of fine structure Mi, Dan-bi of a solemn and elaborate Ming-hua, covered in the other small, and then only have to Wu.
11 Chong (Year 1638) re-Jun-Yuan Temple wells, digging wells from a Late Song Cheng Si Xiao Yuan (the South) written by the "history of heart", a book of poetry to the text in mind when Song Wang Miscellaneous things, be seen as a symbol of national spiritual history.