His father Yu Xuandao (于宣道) was a mid-level official in the legislative bureau of government, the Neishi Sheng (內史省).
As at the time, most of Sui realm was engulfed by agrarian rebellions, he left his post without leave and fled home, to Yong Province.
Li Shimin was created the Prince of Qin, and became his father's most reliable general in fighting the various contenders for supremacy.
Emperor Taizong thereafter specifically issued an invitation addressed to Yu, and also soon bestowed on him the honorific post of Sanqi Changshi (散騎常侍) —which was the third rank, second class—while also making him one of the key staff members for his oldest son Li Chengqian the Crown Prince and creating him the Duke of Liyang.
Eventually, particularly due to fervent opposition by Emperor Taizong's brother-in-law Zhangsun Wuji, the feudal scheme was cancelled.
When he requested that he be allowed to observe the three-year mourning period, Emperor Taizong sent the official Cen Wenben to persuade him otherwise, stating: "In this case, your faithfulness and filial piety may conflict.
On one occasion, when Yu wrote a particularly blunt submission on two matters—Li Chengqian's refusal to allow his staff members to go on vacation, and his reception of the ethnically Tujue man Dageyou (達哥友) into his palace—Li Chengqian became so incensed that he sent the assassins Zhang Sizheng (張思政) and Gegan Chengji (紇干承基) to assassinate Yu.
Once that happened, three key members of Li Zhi's staff—Yu Zhining, Zhang Xingcheng, and Gao Jifu—were promoted to chancellor posts, before Emperor Taizong's death was announced.
(In Yu's case, he was promoted to be Shizhong (侍中), the head of the examination bureau of government, a post considered one for a chancellor.)
Yu was described to be neutral on the matter, while Li Ji stated that it was Emperor Gaozong's own household business.
In 659, Yu requested to retire from his post, and he was made a senior advisor to the new crown prince—Empress Wu's oldest son Li Hong, but continued to carry the designation of a chancellor de facto.
By then, however, Empress Wu's grip on power was firm, and she was taking vengeance on people she believed opposed her ascension, having her ally Xu Jingzong accuse them of having plotted treason.
Their households, as well as that of Han Yuan (who would have suffered execution as well but for the fact that he had already died by the time that executioners arrived at his place of exile), were confiscated to become servants.
In 664, Yu was made the prefect of Hua Prefecture (華州, roughly modern Weinan, Shaanxi), close to the capital, a sign that he had regained some imperial favor, and later that year, he requested retirement, which was granted.