Abstract: Background Vegetation restoration on difficult sites (e.g., saline-alkali lands, karst mountains, arid lands, and mining wastelands) remains strongly constrained by multiple interacting environmental stressors. Despite substantial advances in restoration practices, the effectiveness of vegetation establishment is still limited. The project aims to address three persistent bottlenecks: (1) the scarcity of high-quality, stress-tolerant native germ plasm; (2) the short-term efficacy and high cost of habitat improvement technologies; and (3) the poor structural stability and low ecosystem services of restored plant communities. Methods To address these challenges, this study investigates the biological, soil, and ecological mechanisms underlying vegetation restoration on four representative types of degraded land. The research adopts a four-stage technical framework: identifying key limiting factors, breeding stress-tolerant germ plasm through intelligent selection, enhancing habitat carrying capacity, and constructing efficient forest–grass community systems. This approach integrates multi-scale analyses of gene–phenotype–stress interactions, biochar–microbe–grass synergistic effects, and community assembly processes, aiming to overcome three technological barriers—precise germ plasm breeding, low-disturbance and self-regenerating soil improvement, and sustainable vegetation establishment. Results 1) Identified the gene–phenotype–stress interaction mechanisms of native forest and grass species under multiple environmental stress conditions, and established a stress tolerance evaluation system based on key phenotypic traits and molecular markers to support intelligent germplasm selection and breeding. 2) Clarified the synergistic soil improvement mechanisms of biochar–microbe–native plant systems, and developed low-disturbance and sustainable habitat improvement technologies for soil structure reconstruction, aggregate stabilization, salinity regulation, and fertility enhancement. 3) Revealed the ecological mechanisms of native forest–grass community assembly and structural regulation, and developed near-natural community construction and structural optimization techniques to enhance ecosystem functions on difficult sites. 4) Overcame key technical constraints in stress-tolerant germplasm selection, sustainable habitat modification, and multifunctional community construction, and formed an integrated technical framework characterized by limiting factor identification, intelligent germplasm breeding, habitat carrying capacity enhancement, and efficient community establishment. 5) Established an integrated vegetation restoration technology system for difficult sites that coordinates ecological, economic, and social benefits and supports large-scale ecological restoration and land greening practices. Conclusions This project addresses the major bottlenecks of germplasm scarcity, unsustainable habitat improvement, and unstable community structure, establishing a systematic and efficient technological framework for vegetation restoration on difficult sites. The proposed framework balances ecological, economic, and social benefits and provides essential technical support for China’s national greening initiatives, the Dual-Project (major ecosystem protection and restoration programs), and the Beautiful China initiative, contributing to the development of new productive forces in forestry and advancing China’s ecological civilization strategy.