The invention relates to a method and a system for separating nitrogen from a liquefied natural gas. The system comprises a denitrification tower, a denitrification tower reboiler, a flash tank, an ice chest, a cold separator, an LNG storage tank, a volatile gas compressor and the like. The method comprises the following steps: firstly, cooling a deacidified and dewatered nitrogen-rich natural gas to -145 DEG C to -162 DEG C, throttling and carrying out first separation on nitrogen; carrying out gas-liquid separation in the LNG storage tank to obtain a volatile gas; reheating, compressing and cooling the volatile gas, carrying out cryogenic treatment in the ice chest, then feeding the volatile gas subjected to cryogenic treatment to the denitrification tower to rectify, and carrying out second deep separation on the nitrogen; further cooling an overhead gas, and then carrying out third separation on the nitrogen in the flask tank; and recovering heat from the obtained gas phase to obtain a nitrogen-rich tail gas. According to the method disclosed by the invention, through the processes of twice flash evaporation and once distillation, nitrogen in the liquefied natural gas is removed; the nitrogen content in the product LNG is reduced to below 1%; the nitrogen content in the tail gas reaches 99.9%; and the methane content is reduced to 0.1%. The method disclosed by the invention is good in denitrification effect, and low in energy consumption; the separated nitrogen can be supplemented as a refrigerant or used as plant nitrogen; therefore, the method and the system have good environmental benefits and social benefits.