The invention discloses an II type sterling generator system using ship waste heat. The system comprises a ship smoke discharge system, an II type sterling engine body, a working medium supply and recovery system, a power generation system, a starting system and a control system for controlling the operation of the whole system, wherein the II type sterling engine body comprises a first sterling engine body, a second sterling engine body, a main crankshaft and a flywheel. A high-efficiency waste heat absorber of the II type sterling engine is mounted behind a ship waste gas boiler for further absorbing the ship smoke discharge heat to generate electricity so as to reduce the greenhouse effect caused by the ship smoke discharge. The II type sterling engine is designed with two parallel high-temperature and low-temperature heat regenerators having one-way valves. When helium is transferred by a cold cylinder to a heater, the high-temperature heat regenerator works; when the helium is transferred by a hot cylinder to the cold cylinder through the heater, the low-temperature heat regenerator works; and a PLC controls one of the high-temperature and low-temperature heat regenerators to work, so that the efficiency of the sterling engine is improved.