This study aimed to evaluate and compare the effects of oil- and air-heat treatments on the durability of Paulownia tomentosa and Pinus koraiensis woods against Fomitopsis palustris and Trametes versicolor. The wood samples were treated in palm oil and air at 180, 200, and 220 °C for 2 h. The weight loss, morphology, crystalline properties, and chemical compounds of untreated and heat-treated wood after fungal attack were investigated. The significant difference in weight loss between oil- and air-heat-treated samples was shown at 220 °C. Heat-treated wood exposed to white-rot fungus showed a lower weight loss than that exposed to brown-rot fungus. The cell components in the untreated- and heat-treated Paulownia tomentosa and Pinus koraiensis at 180 °C were severely damaged due to fungal exposure compared to those at 220 °C. A fungal effect on the relative crystallinity was observed in heat-treated wood at 180 °C, whereas the effect was not observed at 220 °C. Following brown-rot fungus exposure, untreated- and heat-treated wood at 180 °C showed a notable change in the Fourier transform infrared (FTIR) peaks of polysaccharides, whereas no noticeable change in lignin peaks was observed. Heat-treated wood at 220 °C showed no noticeable change in the FTIR spectra owing to brown-rot fungus exposure. Exposure to white-rot fungus did not noticeably change the FTIR spectra of untreated and heat-treated wood.