From its location near the famous medieval library of Kanazawa Bunko, it was referred to as Musashi-Kanazawa Domain (武蔵金沢藩, Musashi-Kanazawa-han) or Bushū-Kanazawa Domain (武州金沢藩, Bushū-Kanazawa-han) during the Edo period, although the Kanazawa Bunko itself was not within its territory.

In the han system, Mutsuura was a political and economic abstraction based on periodic cadastral surveys and projected agricultural yields.

The Yonekura clan, former retainers of the Takeda clan of Kai Province, pledged allegiance to Tokugawa Ieyasu after the Takeda were destroyed by Oda Nobunaga, and subsequently served as hatamoto in the Tokugawa shogunate after the Battle of Sekigahara in 1603.

Yonekura Masatada (米倉昌尹) (1637–1699) was favored by Shōgun Tokugawa Tsunayoshi, rising rapidly through the ranks until he reached the post of wakadoshiyori in 1696.

The additional revenues provided by this office propelled him past the 10,000 koku necessary to qualify as a daimyō, and he became the first lord of Mutsuura Domain.