The invention discloses a zero-emission marine combined cooling heating and power supply unit and a using method thereof. The zero-emission marine combined cooling heating and power supply unit comprises a fuel cell stack module, a combustion chamber, a reforming chamber, an air preheating chamber, an air blower, a steam generator, a desulfurization chamber, a storage battery, a regenerative chamber, a water tank, a direct-current converter and the like. The air preheating chamber is respectively connected with the air filtering device, the reforming chamber and a cathode inlet of the stack module; the reforming chamber is respectively connected with the desulfurization chamber and an anode inlet of the stack module; the inlet of the combustion chamber is respectively connected with the cathode and anode outlets of the stack module, the filtering device and the premixing gasification chamber; the combustor outlet is connected with the air preheating chamber; the steam generator is respectively connected with the premixing gasification chamber and the regenerative chamber. The unit further comprises a tail gas gas-liquid separator, a tail gas capturing and sealing cabin, a ship charging and energy storing device, an electric device control cabinet and the like. The unit has the advantages of being free of carbon emission, wide in fuel diversity, high in power generation efficiency, high in comprehensive utilization rate of fuel combined cooling heating and power supply energy, good in economical efficiency and the like.