In 1555 during the reign of Emperor Jiaqing of the Ming Dynasty, a severe earthquake occurred, and the temple was wrecked. It was reconstructed on the base of the original framework of the damaged pagoda around 1560. Despite reconstruction, the pagoda has retained part of its Tang Dynasty style.

Pujiu Temple Pagoda is square, each side of the ground floor measuring 8.05 meters. The door on the south side is 1.28 meters wide. The inside chamber was also probably originally square, but the southern and northern walls are no longer exactly the same length as the eastern and western walls. The door also is not in the exact middle. All this is explained by new bricks, having been added to the original framework during reconstruction. There is a niche on the back wall of the first storey, but the statue of Buddha is missing. No stairs were installed on the first storey; the ceiling is an octagonal dome with a hole in the middle opening to the upper floor. The ceiling is believed to have been reconstructed during the Ming Dynasty. From the second level up, the interior of the pagoda is a hollow tube, without any floor slabs or stairs, but traces of floor slabs can still be observed.