After his death, the Huan clan would be entrenched in the Jin power struction for decades, after his son Huan Xuan temporarily usurped the Jin throne in 403 as the emperor of Chu (楚), he was posthumously honored as Emperor Xuanwu of Chu with the temple name of Taizu (太祖).
When he was young (less than a year old), his father once received a visit from Wen Jiao, who saw the infant boy and thought that the child was special.
As he was considered capable, and his father had died for the imperial cause, he was selected as the husband for Emperor Cheng's sister Sima Xingnan (司馬興男) the Princess Nankang.
He inherited his father's title of "Baron of Wanning", and he gradually rose in rank, eventually becoming the governor of Xu Province (徐州, then modern central Jiangsu).
After Yu's death in 345 (during the reign of Emperor Mu, then a toddler), the chancellor He Chong commissioned Huan to succeed Yu, as the commander of the military forces in the western provinces (roughly modern Hubei, Hunan, Guizhou, and Yunnan), even though some other imperial officials had misgivings about Huan's ambitions and independence.
Soon after taking over for Yu, the ambitious Huan turned his attention west, wanting to destroy Cheng-Han, whose emperor Li Shi had mismanaged his state and lost the trust of his people.
Huan released him and escorted him to the Jin capital Jiankang, where Emperor Mu pardoned him and created him a marquess.
The victory over Cheng-Han, however, brought fear in imperial officials that the ambitious Huan intended to control the government.
Emperor Mu's granduncle Sima Yu, Prince of Kuaiji, in order to counter Huan, invited a renowned official, Yin Hao, to join in major decision-making with him and Cai Mo.
Around the new year 352, Huan, upset that his requests were being repeatedly denied, mobilized his troops and gestured as if he were about to attack the capital.
Yin was shocked, and initially considered either resigning or send the imperial banner of peace (Zouyu Fan, 騶虞幡) to order Huan to stop.
He did not carry out another northern campaign, apparently not willing to face the capable Former Yan general Murong Ke in battle.
Instead, he set up his base at Zheqi (赭圻, in modern Wuhu, Anhui) and monitored the situation at Jiankang remotely.
Despite Xi Chao's advice that he head directly for Former Yan's capital Yecheng, Huan proceeded slowly, defeating Former Yan's troops repeatedly but taking three months to reach the Yellow River, stoppinging Fangtou (枋頭, in modern Hebi, Henan) -- and again hesitated there at crossing the Yellow River and attacking Yecheng, not far away.
Yuan, instead of submitting, occupied Shouchun (壽春, in modern Lu'an, Anhui) and rebelled, seeking assistance from both Former Yan and Former Qin.
Because Emperor Fei had been cautious in his behavior and lacked faults, they decided to spread rumors that Emperor Fei was impotent and unable to bear children—and that his sons, by his concubines Consort Tian and Consort Meng, had in fact been biological sons of men whom he favored, Xiang Long (相龍), Ji Hao (計好), and Zhu Lingbao (朱靈寶).
Meanwhile, he carried out several acts intended to both terrorize imperial officials and to affirm his power—he deposed Emperor Jianwen's brother Sima Xi (司馬唏) the Prince of Wuling, and killed many members of the honored Yin and Yu clans under false accusations of treason.
Indeed, Emperor Jianwen initially drafted a will that stated, "The Grand Marshal Huan Wen shall be regent under the precedent of the Duke of Zhou," and "If the child can be assisted, assist him; otherwise, take the throne yourself," mirroring language that Liu Bei, the founding emperor of Shu Han, used when entrusting his son Liu Shan to Zhuge Liang.
With Huan not in the capital to affirm it, however, Wang Tanzhi persuaded Emperor Jianwen to tear up the will and rewrite the instructions as, "All major affairs shall be submitted to the Grand Marshal, under the precedents of Zhuge Liang and Wang Dao," greatly reducing any legitimacy Huan might have if he should try to take the throne.
As Wang and Xie greeted him, however, he did not carry out the rumored actions, and after visiting the young emperor, returned to his base at Gushu (姑孰, in modern Ma'anshan, Anhui).