While traditional wood preservatives may impede wood decay, their potential harm to both human health and the environment has led to limitations in their usage. This has spurred recent research to focus on seeking wood preservatives derived from plants, owing to their inherently eco-friendly attributes. Agricultural waste such as corn stover fractions, are not only abundant but also frequently underutilized, making them promising candidates for such endeavors. This study delves into the antifungal properties of extracts derived from thermally degraded corn stalk and corn cob. The selection of optimal raw materials and the identification of the most effective thermal degradation process were determined based on their inhibitory activity against Gloeophyllum trabeum (Pers.: Fr.) Murr. and Trametes versicolor (L. ex Fr.) Quél. Gas chromatography-mass spectrometry (GC-MS) was employed to analyze the composition of corn cob extracts resulting from various thermal degradation processes. The evaluation of decay resistance involved wood decay resistance tests and electron microscope observations. Results indicated that ethanol extracts from corn cobs heat-treated at 220 °C exhibited the strongest antifungal activity, accompanied by the highest extract yield. Additionally, the corn cob extracts also demonstrated inhibitory effects on the growth of Aspergillus niger, Escherichia coli, and Staphylococcus aureus. Chemical analysis revealed significant quantities of vanillin, squalene, and other compounds known for their antifungal or antibacterial activity in the corn cob extracts. Furthermore, wood treated with these extracts exhibited improved decay resistance, surpassing that against G. trabeum compared to T. versicolor. These findings suggest that thermally degraded corn cob extracts can be utilized as environmentally friendly wood preservative.