According to The Eunuchs by Tsai Shih-shan Henry, Kaifeng experienced a major Yellow River Flood in 1375; the death toll was roughly 15,000, with most casualties being farmers.

During the Song Dynasty and the early Ming Dynasty, the government constructed numerous small canals to drain the water from the Yellow River. However, war and conflict resulted in negligence towards and the deterioration of the flood control system.

Kaifeng, located several miles south of the Yellow River, was therefore frequently inundated by floods; this figure is as high as fourteen in the Ming Dynasty alone.

Wang Yang-ming (王阳明, 1472–1529), a renowned Neo-Confucian philosopher, explained that the 1375 flood was a prime example of how even a virtuous man can fall victim to the power of nature.

The synagogue was first erected in 1163. It was rebuilt in 1279.

In 1421, it was rebuilt yet again with the imperial permission that was awarded to the community due to Zhao Cheng’s contribution to the regime.

According to the 1679 Stone Inscription, during the Zheng-tung era (正统,1436–1450) of Emperor Ying-zong’s reign (英宗, reign 1435–1449), the synagogue was in a state of decay. Upon seeing this, Li Rong funded the construction of the Front Hall. It was built to be grand and long-lasting (正统中岁又寺基圯坏李荣见其颓捐资建前殿规模宏远).

According to the 1679 Stone Inscription, during the Zheng-tung era (正统,1436–1450) of Emperor Ying-zong’s reign (英宗, reign 1435–1449, 1457–1464), Gao Keng and others worked hard and persistently on the construction of the Rear Hall. The resulting building appeared to be tall and deep, full of gold glitter and various colours. They also built a corridor connecting the Rear Hall to the Front Hall. Thus, both the Front Hall and the Rear Hall were complete (成华中高鏗等力建后殿相疑高深妆金结彩并作穿廊连接前殿前后殿既落成).

According to the 1489 Stone Inscription (弘治碑), in 1461, the Yellow River flood inundated everything, only the foundation of the synagogue bared survived (天顺五年河水淹没基址略存).

The subsequent rebuild of the synagogue led to the commemoration tablet of 1489.

According to the 1489 Stone Inscription (弘治碑), Ai Jing presented a petition to the provincial government, seeking permission to rebuild the synagogue in the same manner in which the government had granted such consent in the year 1279 (艾敬等具呈按照先奉本府承河南布政使司札付等因至元年古刹清真寺). Permission was granted.

According to the 1489 Stone Inscription (弘治碑), Li Rong returned and prepared funds and building materials for the construction of a grander and more beautiful synagogue, to be decorated with gold and a multitude of different colours; it would have a completely new look (李荣复备资财起盖深遂明金五彩妆成焕然一新).

According to the inscription of 1489, during the Tian-shun era (天順, 1457–1464), Shi Bin, Li Rong, Gao Keng and Zhang Xuan obtained a Ningbo Torah; Zhao Ying, from Ningbo, respectfully carried this Torah and brought it to Kaifeng and placed it in the synagogue (天顺年石斌李荣高鏗张瑄取宁波本教道经一部，宁波赵应奉经一部，赍至汴梁归寺).

Jin Xuan (金瑄), a Jew from Ningxia, purchased and donated an offering table, bronze censor, vase, and candle holder to the Kaifeng synagogue.

One of Jin Xuan’s ancestors was the Court President of State Banquets (光禄寺卿). His great-uncle was a commander of the imperial guards.

In 1478, Jin Xuan’s younger brother, Jin Ying (金瑛), purchased a piece of land near the Kaifeng synagogue and donated it to the synagogue (舍资财置寺地一段).

According to the 1489 Stone Inscription (弘治碑), Gao Keng (高鏗), Gao Rui (高锐), and Gao Hong (高宏) provided the materials for and the funding of three additional sections to the Rear Hall of the synagogue (自备资财增建后殿三间).

All new constructions were magnificently infused with gold leaves and variegated colours.

It was this new section that eventually housed the Bethel or the Ark for the Revered Scriptures.

On the outside, a walkway was built to connect the Rear Hall to the Front Hall (外作穿廊接连前殿).

According to the 1663a Stone Inscription (康熙碑a), after the synagogue was destroyed by the Yellow River flood of 1461, funds were raised to restore the synagogue. Thirteen rolls of the Torah, as well as tens of copies each of the Square Scripture and Miscellaneous Scripture, were eventually placed in the new synagogue (明天顺五年黄河水淹没复捐资重修，殿中藏道经一十三部，方经散经各数十册).