This study employs a material flow analysis (MFA) to examine the usage patterns of domestic and imported wood resources in South Korea, analyzing the significant differences in utilization, and their impacts on carbon storage. We found a contrast between manufacturing and industrial uses of domestic and imported wood. Imported wood products with high economic value and longevity are primarily used in sustainable construction and manufacturing. In contrast, domestic wood is primarily utilized in lower-value wood-based boards and energy production, with a shorter lifespan and lower carbon storage potential. This study outlined the economic and environmental value chains by wood origin, highlighting their industrial linkages and utilization pathways. Consequently, tailored strategies are essential to promote sustainable wood resource use and advance climate mitigation. Recommendations have been provided for policy instruments to enhance wood resource management sustainability and climate change mitigation.