The invention relates to a manufacturing method and system of a polyurethane insulation box for a liquefied natural gas ship. The manufacturing method includes a gluing and assembling stage, a leveling and output stage, a CNC machining stage and a packaging stage, wherein the gluing and assembling stage comprises a universal gluing and assembling process, a press-fitting process and an aging process; the manufacturing system comprises a universal gluing and assembling area, a MARK III secondary gluing and assembling area, a press-fitting area, an aging area, a leveling and output area, a CNC machining area and a packaging area. Compared with the prior art, the advantage of high efficiency of automatic equipment is utilized, function blocks are set according to properties of machining processes, all stations in the blocks are connected through an automatic logistics conveying line, all the blocks are connected through an intelligent conveying system, and thus the system can operate continuously, efficiently and orderly, the functions of the blocks can be exerted to the maximum extent, the influence of failures of single equipment on the whole production system is lowered, productionefficiency is improved, the production hours are shortened, and the high-precision quality requirement of products is met.