In one embodiment, an ammonia synthesis system comprising, an ammonia synthesis reactor, a waste heat boiler, a supply water heat exchanger, a recycle gas heat exchanger, a water cooler, an ammonia chiller and refrigeration exchanger, a secondary ammonia chiller, an ammonia separator, a liquid ammonia tank, a recycle compressor and a start-up heater, and wherein, a process gas is heated in the recycle gas heat exchanger and enters the ammonia synthesis reactor and the waste heat boiler, a reacted gas stream exits from a bottom of the waste heat boiler and is cooled in the supply water heat exchanger, a gas stream enters the recycle gas heat exchanger, the water cooler, the ammonia chiller and refrigeration exchanger, the secondary ammonia chiller, and is cooled, the gas stream enters the ammonia separator to form a separate liquid ammonia and the separated liquid ammonia enters the liquid ammonia tank.