Heilongjiang Province, as China’s principal gateway for Russian timber imports, faces structural inefficiencies in the localization of wood-processing enterprises—characterized by ecological sensitivity, resource–industry mismatches, and uneven spatial distribution. To address these challenges, this study proposes a two-stage site selection framework that integrates Geographic Information Systems (GIS) with an enhanced Non-dominated Sorting Genetic Algorithm II (NSGA-II). The model aims to reconcile ecological protection with industrial efficiency by identifying optimal facility locations that minimize environmental impact, reduce construction and logistics costs, and enhance service coverage. Using spatially resolved multi-source datasets—including forest resource distribution, transportation networks, ecological redlines, and socioeconomic indicators—the GIS-based suitability analysis (Stage I) identified 16 candidate zones. Subsequently, a multi-objective optimization model (Stage II) was applied to minimize carbon intensity and cost while maximizing service accessibility. The improved NSGA-II algorithm achieved convergence within 700 iterations, generating 124 Pareto-optimal solutions and enabling a 23.7% reduction in transport-related CO₂ emissions. Beyond carbon mitigation, the model spatializes policy constraints and economic trade-offs into actionable infrastructure plans, contributing to regional sustainability goals and transboundary industrial coordination with Russia. It further demonstrates methodological generalizability for siting logistics-intensive and policy-sensitive facilities in other forestry-based economies. While the model does not yet account for temporal dynamics or agent behaviors, it provides a robust foundation for informed planning under China’s dual-carbon strategy and offers replicable insights for the global forest products supply chain.