Portuguese Jesuit Bento de Gois, who visited Aksu in 1604, described him as 12-year old local ruler and a nephew of Muhammad Khan.
Shudja ad-Din Ahmad Khan was killed in 1618 during hunting when his camp in the mountains was attacked at night by 600 armed men of Muhammad Kasim Shah, ruler of Sarikol.
Previously, Abdurashid Khan (1533–1560) of Yarkand Khanate expelled to India practically all Dughlat Emirs, because regarded them aa a threat to his power.
Shudja ad-Din Ahmad Khan never attempted to perform such radical measures, but tried to reduce the local power of many Emirs and Sultans and to strengthen centralization of power in the hands of a Great Khan of Yarkand, his measures were supported by Churas Emirs, but were met with hate by the others, that cost him his life.
Begs of Kashgar, Yarkand and Yangi Hisar did not recognized him and supported Abdal Latif Sultan, son of killed Khan, as a lawful successor.