Comprehensive land consolidation is a crucial approach for coordinating urban-rural development and promoting rural revitalization, with its core focus on ecological protection and restoration, informed by ecological foundation investigations, to address challenges such as fragmented landscape patterns, low biodiversity, and agricultural non-point source pollution in rural areas. Taking the pilot area of comprehensive land consolidation in Langxia Town, Jinshan District, Shanghai City as a case study, this research integrated the concepts of Nature-based Solutions (NbS) and Other Effective area-based Conservation Measures (OECMs). Based on ecological foundation investigation results, an ecological restoration functional zoning system centered on “ecological source areas-ecological corridors-ecological restoration nodes” was constructed, forming four functional zones (ecological wilderness area, ecological priority area, ecological agricultural area, and ecological symbiotic area) and an integrated agro-forest-water composite ecological corridor. By applying ecological restoration toolbox technologies, including water ecosystem governance, near-natural forest restoration, and the integration of gray-green infrastructure, three typical demonstration zones were established, significantly enhancing habitat quality and biodiversity. Post-restoration results show an annual increase in ecological value of approximately 4.04 million yuan, with 32 hm2 of newly added wetland functional areas and 1.61 million cubic meters of non-point source wastewater purified. The habitats of indicator species such as black-spotted frogs and cattle egrets will notably be optimized. This study offers a systematic approach to ecological protection and sustainable agricultural development in metropolitan peri-urban areas, highlighting the importance of ecological foundation investigation in informing comprehensive land consolidation.