Two integrated harvesting methods have been primarily applied to increase the opportunity for forest biomass utilization. In Korea, small shovels with a carrier for cut-to-length harvesting (CTL system) and tower yarders for whole-tree harvesting (WT system) are commonly used for the transportation of tree assortments (i.e., sawlogs and logging residue). No previous studies are available in South Korea that have compared and highlighted the operational performance and yield of logging residues between the CTL and WT harvesting systems. Thus, our study’s main objectives were to (1) evaluate the productivity and costs of the two harvesting systems through a standard time study method and (2) estimate the amount of harvesting logging residue at the landing. The productivities of the CTL and WT systems were 1.45 and 2.99 oven-dried tons (odt)/productive machine hour (PMH), at a cost of 86.81 and 45.41 USD/odt, respectively. In the WT system, the amount of logging residue (2.1 odt/ha) collected at the landing was approximately four-times larger than that of the CTL system (0.5 odt/ha). Our results suggested that the WT system is a less expensive and more suitable system when there are markets demanding logs and biomass, whereas the CTL system remains a less expensive option for stem-only harvesting. Furthermore, these results are important for estimating the economic and environmental amount of residue that could be potentially recovered and utilized from the forest types included in the study.