The invention discloses a device and method for cooling partial high heat flow within a limited space. The device comprises a lower cover board, a water inlet pipeline, an inlet pipeline connector, a vacuum pumping port, an upper cover board, a supporting column, a containing space, a super-hydrophilic micro-nano structural coating, an evaporation area, a micro-channel tube bundle, an outlet pipeline connector, a water outlet pipeline, a partial heating source, a base board and a micro-channel hole. The micro-channel tube bundle is arranged in the condensation section space of an internal pipe of a guide panel heat pipe, so that the space of a whole cooler device is largely reduced. Due to the arrangement of micro-channel tubes, the cooling superficial area is enlarged, the coefficient of heat exchange is increased through forced convection of water in the micro-channel tubes, and the heat exchange capability of the condensation end is enhanced. The boiling heat exchange capability of the evaporation area is enhanced through the super-hydrophilic micro-nano structural coating, and finally the overall heat exchange capability of the device is enhanced.