With the spread of COVID-19 in Japan，the Japanese government shifted the focus of epidemic prevention and control from “port control” to “local control” in January 2020，and ever since the local governments have been playing the leading role. However，as of the first half of 2021，Japan is still mired in repeated outbreaks，its epidemic prevention and control facing problems such as “long fronts，poor results，and constant rebound”. This paper argues that it is a “microcosm” of the difficulties in the debugging process of central-local relations after the decentralization reforms in Japan that began in the 1990s and have since expanded the authority and financial resources of local governments，pushing the central-local relations from “up and down，master and subordinate” to “equal and cooperative” by reducing the central government’s intervention in local governments. After two decentralization reforms，the reciprocity between local governments and the central government has increased to a certain extent. But in response to COVID-19 have emerged such problems as unclear division of labor between the central and local governments，lack of local finance，and excessive integration of central and local administrative affairs，which collectively reveal that the current decentralization reforms in Japan have not achieved the original purpose.