The coupled carbon and nitrogen (C-N) cycles, essential to Earth’s life support systems, face increasing disruption from global change drivers, with profound implications for climate, ecosystems, and human well-being. To enable cost-effective global C-N management, we developed the Coupled Human and Natural Systems-Carbon and Nitrogen cycles (CHANS-CN) model. This global-scale tool quantifies C-N fluxes, analyzes interactions across 16 human-natural subsystems, and assesses impacts of climate change, urbanization, and international trade. We further established a novel Cost-Benefit framework for integrated C-N management and pioneered the Nitrogen Credit System (NCS) to incentivize mitigation. Collectively, the CHANS-CN model, cost-benefit framework, and NCS—augmented by adaptive measures—deliver scientific support for reconciling global food security, environmental protection, and sustainable development.