The present invention is directed to provide an operation method for a micro-cogeneration system that enables the use of heat recovered from a cogenerator for both space heating and generating hot water by connecting the cogenerator and a heat transfer medium channel of the boiler, thereby reducing the cost required for operating the cogeneration system, and facilitates the control of heat to be supplied in heating mode and in hot water mode. To this end, the present invention comprises: operating a cogenerator (100) having a heat exchanger (110) for recovering waste heat that is produced during the power generation; performing a control operation in such a manner that a heat transfer medium supplied from the cogenerator (100) is stored in a heat transfer medium reservoir tank (300) after going through a boiler (200) connected to the heat exchanger (110), and the heat transfer medium stored in the heat transfer medium reservoir tank (300) is circulated into the heat exchanger (110) of the cogenerator (100); operating only the cogenerator (100) when there is no heating and hot water loads; and stopping the operation of the cogenerator (100) if it is determined that the temperature of the heat transfer medium inside the heat transfer medium reservoir tank (300) has reached a preset temperature.