Cercidiphyllum magnificum is, along with C. japonicum, one of only two members of the genus Cercidiphyllum and family Cercidiphyllaceae. It was first described as a variety, C. japonicum var. magnificum, in 1919 by Japanese botanist Takenoshin Nakai, then separated into a different species the following year in his Catalogus seminum et sporarum Hortus Botanicus Universitatis Imperialis Tokyoensis. The type locality is from Honshu, Japan in the Ashio Mountains (Mount Nikkō-Shirane and Mount Konsei.