We reconstructed the tectono-metamorphic evolution of the low-grade metamorphosed Cretaceous Shimanto accretionary complex in the Kanto Mountains, Central Japan, based on radiolarian fossils, metamorphic temperatures derived from illite crystallinity analysis, and timing of metamorphism based on illite K–Ar dating. The accretionary age of the Kobotoke Group is Turonian to Maastrichtian (66–94 Ma), based on radiolarian fossils. Illite crystallinity data indicate metamorphic temperatures of approximately 300 °C. The illite K–Ar ages constrain the timing of metamorphism to the Middle Eocene around 40 Ma. Combining our results and previous study, we defined two types of low-grade metamorphism within Cretaceous Shimanto accretionary complex of the Kanto Mountains. The early metamorphism, in excess of 300 °C, was related to the uplift of the Sambagawa metamorphic rocks, in turn associated with the subduction of the Kula–Pacific ridge during the Late Cretaceous (65–75 Ma). This metamorphism is recorded in the Otaki Group within the northernmost part of the complex in the Kanto Mountains. Subsequent to the subduction of the Kula–Pacific ridge, a later period of metamorphism, recorded in the Kobotoke Group, is characterized by the thermal effects of the subduction of the young, hot Pacific Plate during the Middle Eocene. The effect of the early metamorphism occurred synchronously 500 km along the trench from Southwest to Central Japan. The later metamorphism occurred at 50 Ma in Kyushu and Shikoku of Southwest Japan, and at 40 Ma in the Kanto Mountains of Central Japan. This difference in the timing of metamorphism between Southwest and Central Japan is explained by the northward migration of the young, hot Pacific Plate.