[citation needed] Shah Jahan sought refuge in Thatta from his father, Emperor Jahangir, after he had rebelled against him.

[4] Shah Jahan was impressed by the hospitality he received by the Sindhi people, and ordered construction of the mosque as a token of gratitude.

[1][5] Construction of the mosque may have also been partially motivated by a desire to help alleviate the effects of a devastating storm that impacted the region in 1637,[3] and which had nearly destroyed Thatta.

The Sufi mystic, Makhdum Nooh, who is buried in the nearby city of Hala is said to have been approached by the mosque's planners in order to correct its alignment.

Popular tradition maintains that Makhdum Nooh then corrected the error overnight by the power of his prayer, thereby ensuring his status as a saint.

[8] The mosque is characterized by extensive brickwork and the use of blue tiles, both of which were directly influenced by Timurid architectural styles from Central Asia[3][1] − from where the previous rulers of Sindh, the Tarkhans, had hailed before the region was annexed by the Mughals in 1592.

The mosque's dome is embellished with exquisite blue and white tile-work arranged in stellated patterns to represent the heavens.

The main prayer hall is set to the west of its central courtyard, which features iwans, or portals, in each of its four cardinal directions.