Disclosed is an apparatus and method of preparing synthetic fuel using natural gas extracted from a stranded gas field on land or at sea as a raw material through a compact GTL process or a GTL-FPSO process. A parallel-type gas purification unit for controlling a molar ratio of synthetic gas and a concentration of carbon dioxide in the synthetic gas, in which a CO2 separation device and a bypass unit are disposed in parallel, is provided and, thus, the gas purification unit may prepare the synthetic gas by a steam carbon dioxide reforming (SCR) reaction using natural gas having different CO2 contents of various stranded gas fields and then supply the synthetic gas having an optimum composition suitable for a Fischer-Tropsch synthesis.