Zoning is vital for balancing biodiversity conservation and sustainable development in protected areas, yet traditional approaches often lead to ecological overprotection and social conflict. This study introduces an integrative modeling framework to optimize zoning strategies in the Longbao Reserve on the Qinghai–Tibet Plateau. We employed MaxEnt and Random Forest algorithms to evaluate habitat suitability for two flagship species: the bar-headed goose (Anser indicus) and the black-necked crane (Grus nigricollis). Results showed that 7.9% of the reserve comprised highly suitable habitats, mainly in the southeast, characterized by wetlands, water proximity, and low human disturbance. Land use and June NDVI emerged as key predictors, contributing over 30% and 35% to model performance, respectively. Based on habitat suitability and current zoning mismatches, we propose a revised four-tier zoning scheme: Core Habitat Conservation (16.9%), Ecological Rehabilitation (7.2%), Ecological Management (53.5%), and Sustainable Utilization Zones (22.4%). This refined framework aligns conservation priorities with local development needs and offers a scalable approach to adaptive protected area management.