The global transition toward renewable and low-carbon energy systems has accelerated large-scale investment in renewable generation, storage technologies, hydrogen infrastructure, and grid modernization. Despite rapid capacity expansion and declining technology costs, emerging green energy ecosystems continue to exhibit infrastructure underutilization, supply concentration risks, cost volatility, and uneven emission effectiveness. This paper argues that these outcomes stem not from insufficient scale, but from misalignment among critical system layers. Building on sustainability transition theory, supply chain resilience research, and industrial ecosystem alignment concepts, the study develops the Sustainability–Resilience Gap framework. The framework conceptualizes green energy systems as multi-layer ecosystems requiring synchronized development across structural sustainability, operational resilience, and market absorption capacity. A comparative ecosystem modeling approach evaluates performance divergence across alternative alignment configurations over a ten-year transition horizon under structured disruption scenarios, including mineral supply shocks, grid intermittency stress, regulatory volatility, and demand fluctuation. Results indicate that structural capacity alone explains only part of emission performance variance, while balanced alignment across infrastructure, resilience diversification, and synchronized demand integration significantly improves utilization stability and reduces disruption losses.