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Rational and scientifically based boundary delimitation and functional zoning is a key approach to achieving multi-objective management and differentiated control in national parks. However, existing planning methods often overlook the nonlinear relationships and interactions among various ecological functions, limiting their ability to support refined management. In response to the core objectives of national parks in maintaining ecosystem functions and conserving biodiversity, this study developed an integrated framework combining species distribution modeling, systematic conservation planning, and ecosystem service assessment to optimize the spatial conservation layout of Ailao Mountain and Wuliang Mountain National Park (AWNP). Habitat suitability for four key species was modeled using the MaxEnt algorithm, which showed high predictive accuracy (AUC>0.97). Using Marxan, 408 priority conservation units were identified, revealing a conservation gap of 302.10 km2. The optimized park area was 1796.51 km2, significantly enhancing both conservation coverage and spatial efficiency. Ecosystem services including water yield, carbon storage, habitat quality, sediment delivery ratio, and recreational potential exhibited strong spatial heterogeneity, with total ecosystem services (TES) forming a distribution pattern of "high in the center and low at both ends." A Restricted Cubic Spline (RCS) model revealed nonlinear relationships and critical thresholds between TES and species habitat suitability. Based on these insights, level I functional zones were delineated, including core conservation zones (1041.48 km2, 57.97%) and general control zones (755.03 km2, 42.03%). Furthermore, K-means++ clustering subdivided the park into four level II functional zones: ecologically vulnerable zones, ecological restoration zones, ecological control zones, and recreational potential zones. This hierarchical functional zoning approach enables refined management and multi-objective coordination. The zoning method proposed in this study provides a robust scientific foundation for integrating biodiversity conservation with ecosystem service provision. It offers a replicable framework for national park planning and adaptive management of mountain ecosystems.