The invention discloses a ship engine waste heat power generation comprehensive utilization method. The ship engine waste heat power generation comprehensive utilization method comprises the following steps: (1) a flue gas evaporator is arranged on a flue gas exhausting channel of a ship heat-conduction oil furnace, and high-temperature flue gas passes through a shell pass of the flue gas evaporator; a power generation medium of a waste heat power generation system passes through the shell pass of the flue gas evaporator, and the power generation medium is subjected to heat exchange and heat suction with the high-temperature flue gas; meanwhile, cylinder sleeve cooling circulating water of a ship engine set enters a shell pass of a pipe shell type evaporator and is subjected to heat exchange with the power generation medium entering the shell pass of the pipe shell type evaporator of the waste heat power generation system; (2) after the power generation medium is evaporated, the power generation medium is changed into high-temperature and high-pressure steam and is conveyed into an expansion machine, and the expansion machine is propelled to output mechanical power so as to drive a three-phase asynchronous motor to generate power; (3) then the power generation medium enters an underwater condenser outside a board; (4) the condensed power generation medium passes through a fully-closed underwater medium pressurizer to be divided into two paths, namely one path is returned back to the flue gas evaporator, and the other path is returned back to the pipe shell type evaporator. With the adoption of the method, the purification efficiency of a power generation system is improved.