Matsutake (Tricholoma matsutake) mushroom has been favored by Japanese over thousands of years. Due to its high economic value, extensive research has been conducted on matsutake mushroom in Japan over past century. However, few studies have systematically discussed the ecology, cultural, and economic values of this mushroom in Japan. Here, we summarize the colonies development, cultural, and economic values of this mushroom based on our previous findings, government data, and publications. We found that novel colonies were established where organic layers were removed, and pine trees were regenerated. Higher temperatures could enhance the expansion rate of the colony, which in turn could lead to higher matsutake yields especially in cold region. Over past 60 years, the annual production of matsutake has decreased from 3500 tons to a few tens of tons. This decrease in matsutake production mainly caused by reduced woody fuel extraction, pine wilt disease, and climate change. Consequently, Japan has become the world largest importer of matsutake, with largest matsutake imported from China. It is advocated that sustainable utilization of matsutake mushroom in Japan should be considered by various stakeholders along the trade routes.