Ishikawa Mitsuyoshi, the daimyo of Inuyama Castle, who joined the West Army at the Battle of Sekigahara in 1600, was deprived of his fief, and instead, Matsudaira Tadayoshi the fourth son of Tokugawa Ieyasu, who joined the Kiyosu Domain, entered Owari with 520,000 koku.

After that, Ieyasu's ninth son, Tokugawa Yoshinao, ruled Owari as the lord of the Owari Domain, and Hiraiwa Chikakichi, a senior vassal of the Tokugawa clan, entered Inuyama Castle with 113,000 koku (93,000 koku according to one theory) as Yoshinao's chief retainer.

However, in 1611, Chikayoshi died of illness without an heir, and according to his will, his territory was absorbed by the Owari Domain (however, in the history of the Inuyama Domain, Hiraiwa Yoshinori succeeded Chikayoshi and ruled until 1617).

In January 1868, due to the new government's Ishin-Ritsuhan, the Inuyama Naruse clan officially became the lord of the Inuyama Domain and became independent from the Owari Domain of the Owari Tokugawa clan.

The Inuyama Domain was controlled by three families: Ogasawara, Hiraiwa, and Naruse.