Matuyama, who was born at Uyeda (now Usa) in Japan, was the son of a Zen abbot. He was educated at the University of Hiroshima and the Imperial University in Kyoto, where he was appointed to a lectureship in 1913. After spending the period 1919–21 at the University of Chicago working with Thomas Chamberlin he was made professor of theoretical geology at the Imperial University.

He conducted a gravity survey of Japan during the period 1927–32, extending this to also cover Korea and Manchuria, and studied marine gravity using the Vening–Meinesz pendulum apparatus in a submarine.

Matuyama made a significant discovery of the Earth's magnetic field and announced this in his paper On the Direction of Magnetization of Basalt (1929). From studying the remnant magnetization of some rocks he observed that it had appeared that the Earth's magnetic field had changed, even reversing itself in comparatively short times. The period between the late Pliocene and the mid Pleistocene during which the field appeared to be opposite to present conditions became known as the Matuyama reversed epoch. This reversed polarity, particularly as shown by the rocks of the ocean floor, was to prove crucial evidence for the sea-floor spreading hypothesis of Harry H. Hess.