The temple was named after the ancestries of Cloistered Emperor Kameyama and Go-Uda to become 'Daikakuji-to' before changing 'Jimyoin-to' after the ancestry of Emperor Go-Fukakusa.
亀山法皇・後宇多法皇の系統は当寺にちなんで「大覚寺統」と呼ばれ、後深草天皇の系統の「持明院統」と交代で帝位についた。