Located at the easternmost of the mausoleum area, the mausoleum is the main body at Afaq Khoja Mausoleum. The bottom is 35 meters long and 29 meters wide. At the four corners of the mausoleum, there is a tower in a shape of circular column which is half embedded in the wall. The exterior of the dome is covered with green glazed bricks, and the towers and façade are a harmonious combination of yellow-and-green glazed bricks and white walls. The gate is painted with delicate patterns, and the walls on both sides are decorated with beige plaster ornamental design which is exquisitely carved. The interior is painted white.

In the west of the mausoleum area stand a large mosque, a small mosque and a preaching hall. During the Islam festivals, Muslims always do worshiping at the large mosque. The outer hall is in a corridor style. The eaves are supported by more than 70 wooden columns carved with different patterns, making it spacious and spectacular. The small mosque is situated between the large mosque and the mausoleum. The small mosque is for the members of the clan to worship on weekdays. The apse is a dome covered with green glazed tiles, 11.6 meters in diameter and 16 meters high