Born in 1421 as the son of Kono Michimoto, a member of the Kono clan that served as constables (shugo) of Iyo Province. He became head of the Kono clan's Yoshu branch and fought bitterly with the main line's Kono Noritsu over the constableship of Iyo. He was first appointed constable in 1449, only to be replaced by Noritsu the following year, and over his lifetime he was appointed and stripped of the post four times — in 1449, 1453, 1459, and again in 1477 after the Onin War. During the Onin War he allied with the Western army against the shogunate and the Hosokawa. In 1478, he suffered defeat against Noritsu's forces in Wake District, Iyo, and his power waned. In his final years he based himself at Minatoyama Castle, overlooking the port of Mitsu in Iyo, where he died of illness on August 28, 1482, at age 62. His son Michiatsu succeeded him, but the castle is said to have soon fallen to the main line.

A tenacious political survivor who spent his life contesting the constableship with his own kin. Rising to power and losing it four times over, he never gave up the fight — but this prolonged internal strife is said to have sapped the Kono clan's strength, one reason it failed to transform into a full-fledged Sengoku daimyo house.

The ruins of Minatoyama Castle, associated with the Kono naval forces, are preserved today as a historic park. The prolonged conflict between Michiharu and Noritsu is seen as having weakened Kono governance, a distant cause of the clan's later decline in the Sengoku period.