This study analyzed the structural performance of a microalgae-based lightweight ecological integration system for large-span structures to achieve carbon neutrality. To address the load problems of existing soil-based ecological systems, a lightweight system utilizing microalgae bioreactors was proposed, and structural performance was evaluated for four types of large-span structures: truss, arch, dome, and cable structures. Structural analysis results through finite element analysis showed that the proposed system achieved a 70% load reduction effect compared to existing systems, with structural performance improvements including 35-40% reduction in maximum deflection, 30-35% reduction in maximum stress, and 25-30% increase in natural frequency. Environmental performance analysis confirmed CO₂absorption capacity of 12-18 kg per m² annually and PM2.5 reduction effects of 15-25%. Economic analysis results indicated that benefits of 3.95-6.7 million KRW per year are generated for a 1,000 m²reference area, creating cumulative benefits of 179.75-227.5 million KRW over 25 years. Verification through the German BIQ House case confirmed CO₂reduction performance of 6 tons per year for 200 m², demonstrating the practical applicability of the system. This study presented the potential of an innovative ecological integration system that can ensure structural safety of large-span structures while simultaneously contributing to carbon neutrality.