A little over ten years after the flood, in 1653, the Jewish community moved from the north bank of the Yellow River back to Kaifeng. Rabbi Li Zhen and Zhao Zhong-yun were in charge of the safe return of the Jewish scriptures.

According to the 1663a Stone Inscription, in 1653, Gao Xuan (Doctorate Degree), Gao Wei-ping (Licentiate Degree), Li Fa-tian (李法天), and some others drafted a petition to request permission to rebuild the synagogue. It asked permission for the synagogue to be rebuilt in the same place in the same way; this was presented to many different government departments (尔时贡士高选等，生员高维屏李法天等，具呈各衙门请示，按照古刹清真寺准复修理).

The petition was presented to various government agencies.

While waiting for formal approval, they assembled a team to survey the ruins and locate the original layout and dimension of the synagogue. Then, they started fundraising and began the project. It would be ten years before the construction would be complete; it was not until then that Emperor Kang-xi began to rebuild the city of Kaifeng.

The faith and dedication of the Kaifeng Jews had them lead the construction of the centre of their religious life ten years ahead of the country, starting to build back the metropolis of Kaifeng.

Fortunately, the Jewish community was well to do financially and well connected socially before the flood. Thus, their application to the government to rebuild the centre of their religious life was formally approved.

The local authorities presented the Jewish community with two Imperial Tablets to be hung inside the synagogue as a gesture of approval and well wishes.

The Ai Clan Memorial Archway was built in the courtyard of the Front Hall, next to the Second Gate, inside the second enclosure of the synagogue complex.

It was made of wooden pillars, rested on a stone pedestal, and roofed over with green tiles.

The Ai Clan was more prosperous in the Great Ming Dynasty. They led the community in petitioning the government to rebuild the synagogue four times.