In this study, the wood vinegar was made from Cryptomeria japonica using steel kiln. The 4 kinds of fractions including ether-extracted wood vinegar, acidic, phenolic and neutral compounds of wood vinegar were obtained by partition method. The decay resistance of white-rot fungus, Lenzites betulina andbrown-rot fungus, Laetiporus sulphureus with different concentrations of the 4 kinds organic compounds by wood block test of 90 days using C. japonica sapwood as tested wood materials was evaluated as well as the chemical structure changes of the decay wood was also analyzed by Fourier transform infrared spectroscopy (FT-IR) andthermogravimetric analysis (TGA). The results showed that the 1.0% neutral compounds and 1.0% phenolic compounds had the best decay resistance for white-rot fungus, L. betulina andbrown-rot fungus, L. sulphureus respectively, however, there were slightly inferior to that of commercial ACQ agent. According to the FT-IR analysis, the 1.0% ACQ and neutral compounds could protect the lignin and cellulose of wood avoiding destroying by the L. betulina fungus. In addition, the cellulose of 1.0% ACQ and phenolic compounds treated wood was only slightly destroyed by the L. sulphureus fungus and the result was also conformed to the TGA analysis.