Born in Hefei as ''Duan Qirui'' , his courtesy name was ''Zhiquan'' . His grandfather was Duan Pei , an officer in Li Hongzhang's privately raised army called Huai Army . Duan Qirui's father died early and Duan Qirui was raised by his maternal grandmother.
In 1885, Duan Qirui entered Tianjin military academy specializing in artillery, and graduated in 1889. After graduation, he was sent to Lushun to oversee the construction of artillery fortifications, and soon, Li Hongzhang sent him to study military science in , and after returning to China, he was first named as a commissioner of Beiyang Armory and then as an instructor of Weihai military academy. In early 1896, Yuan Shikai named Duan Qirui as the artillery commander of his new army and inspector general of training, so Duan had become one of Yuan Shikai's top lieutenants.
Duan later opposed Yuan's bid for - he expected to succeed Yuan in the presidency, but the imperial gambit was seen as a betrayal. Duan tried to play the intermediary between the and Yuan, just as Yuan had done during the Xinhai Revolution. Their friendship never repaired even after he was given the , because Yuan shrewdly stripped that office of its powers. He served as premier intermittently from 1912 to 1918 under several governments as part of shaky coalitions that often collapsed. Duan formed the Anhui clique when the Beiyang army fractured after Yuan's death, and was the strongest supporter of China's entry into World War I, but was unwilling to send any of his own troops abroad since it would weaken him against his rivals.
After being fired by President Li Yuanhong for obtaining secret Japanese loans in 1917, he regained his office by toppling 's restoration attempt of Puyi. He was also engaged in a power struggle against his archrival, President Feng Guozhang, over the war with Sun Yat-sen's rival government. Duan wanted a military solution while the president advocated negotiating. He is most noticeable for his frequent collaboration with the Japanese in return for military and financial aid. His promise of giving Japan German concessions in Shandong was one of the reasons for the May Fourth Movement in Beijing. He was held responsible for granting Japan its 21 demands in 1915, one of which was the Shandong issue. With his popularity gone, other warlords led by Cao Kun sided against him and on July 14, 1920, Duan's troop clashed with troops of Zhili clique. After a merely four days, Duan suffered a decisive defeat and he was forced to retire. Duan fled to Japanese settlement in Tianjin and became an apartment landlord. While out of power, his Anhui clique allies were rapidly losing ground. In 1923, he joined the chorus against Cao Kun's assumption of the presidency. Zhejiang, the last Anhui held province, fell in the summer of 1924.
He was called out of retirement in November 1924 after the Beijing coup and put in charge of a provisional government after an agreement with Zhang Zuolin and Feng Yuxiang. Duan, Zhang, and Feng were negotiating with Sun Yat-sen on national reunification until the latter succumbed to cancer in 1925. With his clique's military power in shambles, his government was hopelessly dependent on Feng and Zhang. Knowing that those two had poor relations, he tried to play sides secretly. On March 18, 1926 he ordered his troops to gun down protesters, killing dozens in what became known as the March 18 Massacre. The next month, Feng deposed Duan who then fled into Zhang's hands. Zhang, tired of his double-dealings, refused to restore Duan after capturing Beijing. Most of the Anhui clique had already sided with Zhang. He fled to Tianjin and later moved to Shanghai where he died.
Go, Buddhism and vegetarianism
Duan was also well known as a player and patron of . He usually won because his opponents feared defeating him, with an exception of his own son, who was also a patron of and was not afraid of defeating his own father. After Duan's complete defeat, he became a devoted Buddhist, built a worship hall within his own home, and prayed every morning. Many of his former subordinates frequently came to pray with him. On the first and the fifteenth days of each month , Duan would go to temples to participate in various Buddhist events. Duan became a vegetarian; douchi was his favorite food and was served at every meal. Duan also kept a hen farm at home to provide him with eggs, but kept no roosters, as he claimed that without fertilization, the eggs remained vegetarian.