The invention provides a manufacturing method of a stainless steel cooler for a Stirling engine. The manufacturing method comprises the following steps: machining parts of the stainless steel cooler according to a drawing size; washing the parts; assembling upper and lower pipe plates and a shell, and welding an electron beam; assembling a cooling pipe and pre-setting brazing filler metal; brazing in vacuum; and machining and checking a whole machine. By compounding two process of vacuum electron beam welding and vacuum brazing, precision welding and molding of the stainless steel cooler can be realized, and the whole size precision of a product is guaranteed; uniform and quantitative coating of pasty brazing filler metal is realized through coating pasty nickel-based brazing filler metal by adopting a pneumatic dispensing machine, the coating efficiency is improved, and the corresponding brazing filler metal cost is reduced; and obtained brazing seams are full and smooth, and the consistency of welding is improved. The manufacturing method is simple in process, high in welding precision and low in cost, the yield of the product is greatly improved, and the prepared stainless steel cooler is reliable to operate and convenient to mount and repair.