Upon succession, he appointed his younger brother Ashina Kutou (阿史那庫頭) as lesser khagan in the east.
Around the new year 554, after defeat of Yujiulü Kangti at the hands of Göktürks, the remnants of Rouran, which by that point was near its end, surrendered to Northern Qi to seek protection from Gökturk attacks.
Siege was a success as Tuyuhun king Murong Kualu's wife, children and treasure was captured, but he returned to his homeland after the Turks withdrew.
He then further defeated the Hephthalites to the west near Bukhara in 557 together with Khosrow I, however this battle was largely overseen by Muqan's uncle Istami.
Ultimately, Emperor Wu of Northern Zhou took the extra step of dispatching Yang Jian, the Governor of Liangzhou, along with Wang Qing (王庆) and others to formally propose the marriage.
In spring 565, Emperor Wu sent his brother Yuwen Chun (宇文純), Yuwen Gui (宇文貴), Dou Yi (竇毅) and Yang Jian (楊薦) to lead a ceremonial guard corps to Tujue to welcome back Muqan's daughter for marriage to him.
In spring 568, a major storm at Göktürks' headquarters inflicted substantial damage, and Muqan Qaghan took it as a sign of divine displeasure at his rescission of the marriage agreement with Northern Zhou.
A complete genetic analysis of Muqan Qaghan's daughter Empress Ashina (551–582) in 2023 by Xiaoming Yang et al. found nearly exclusively Ancient Northeast Asian ancestry (97,7%) next to minor West-Eurasian components (2,7%), and no Chinese ("Yellow River") admixture.
This caused difficulties for his son Talopien, as he was born to a non-Turkic woman who Muhan married as part of diplomatic relations with other states.