The invention discloses an ammonia carbon-free synthesis system by means of nuclear energy and a method thereof .The system comprises a high-temperature gas cooled reactor, a steam generator, an overheater, a solid oxide electrolytic cell, a Stirling hot air engine, a heater, a mixer, a deep cooling air separation unit, a low-pressure compressor, an intercooler, a high-pressure compressor, a preheater, an ammonia synthesis tower, an ammonia condenser, an ammonia separator, a water supply pipeline and an air pipeline .The nuclear energy serves as fuel, air and water serve as raw materials, and the ammonia synthesis system which does not depend on fossil energy or generate pollutants is achieved jointly through the high-temperature gas cooled reactor in cooperation with a steam electrolysis method and a deep cooling air separation method .Waste heat of high-temperature hydrogen generated through the steam electrolysis method is used for driving the Stirling hot air engine to drive the compressors to act, low-temperature nitrogen of the deep cooling air separation unit serves as a cooling medium of the ammonia condenser and the intercooler, the advantages of comprehensively utilizing energy, saving water, simplifying the technological process and the like are achieved, and therefore high economic and environment-friendly value and good application prospects are achieved .