Nitrogen (N) loss and inefficiency threaten both food security and environmental sustainability in tropical agriculture. Despite growing N inputs, many tropical systems suffer from low N use efficiency (NUE) and high pollution due to poor management. Aligning agricultural productivity with environmental safety remains a major challenge, given the lack of integrated, context-specific decision-support approaches. Here, we present a systematic multi-level integration framework to assess the N carrying capacity required to meet crop productivity while staying within safe N surplus limits, enabling a hierarchy of strategic interventions—including N fertilizer quotas, 4R-plus stewardship, and integrated crop-livestock systems. Using Hainan Island, China, as a representative case, we demonstrate that achieving N carrying capacity, target NUE levels, and halving N losses requires combining optimized cropland management with enhanced internal nutrient recycling. Scenario analysis shows that integrated strategies can increase NUE by up to 26 percentage points (from 23% to 49%) and reduce synthetic N input by nearly 50%. This work offers a scalable pathway to support evidence-based technological and policy solutions for sustainable N management in tropical agriculture.