Proper forest management can significantly contribute to global or regional carbon neutrality goals; however, the effects of different harvesting strategies on the carbon balances of forest sectors are still not clear. The motivation of this study was to develop a simulation–optimization system that can concurrently maximize the total economic benefits from timber production, biofuel production, and carbon balancing under four alternative harvesting scenarios. The current strict protection strategy (NoCutting) in this region was set as the reference scenario, and the NoConstraints and EvenFlow scenarios were generated based on whether they included restrictions on the flow of harvest volume over time. A final scenario (PreDefine) was inspired by the management policy that was implemented in this region prior to the 2010s. The scenarios were applied to a 123,400 ha boreal forest in Northeast China over a 100 year horizon. All relevant carbon pools within the forestry sector, as well as the avoided emissions related to the substitution effects of using wood products and biofuels, were considered. The results indicated that increasing harvesting intensities significantly improved the carbon balances (1.6 to 5.1 times greater), carbon stock (1% to 7.1% greater) and profitability (1.33 to 4.95 times greater), during which scenario EvenFlow was the first-rank harvest scenario. Hereinto, the carbon balances of the forest under EvenFlow were increased by 0.57 ton ha−1 yr−1 in total, during which the net atmospheric benefits from forest ecosystems, wood productions and substitutions were approximately 0.05, 0.24, and 0.38 ton ha−1 yr−1, respectively, while approximately 0.09 and 0.01 ton ha−1 yr−1 were lost by using the bio and fossil fuels, respectively, during the planning period when compared with NoCutting. The sensitivity analysis revealed that both carbon prices and substitution rates have positive effects on the total carbon balances, while significant negative effects were observed for discount rates. Overall, our results highlighted that periodic harvests rather than passive conservation should be a priority for the sustainable management of boreal forests in Northeast China.