Balancing ecological conservation with agricultural production in protected areas remains a critical challenge, particularly regarding the nexus of food, water, land, and ecosystems (FWLE). Yet, the spatiotemporal trade-offs, synergies, and underlying drivers within the FWLE remain poorly understood. Focusing on the Henan Funiu Mountain National Nature Reserve (HFMNNR), we quantified water yield (WY), habitat quality (HQ), and food production (FP) using the InVEST model and statistical yearbook data. The XGBoost-SHAP framework was applied to dissect the key drivers and mechanisms governing the FWLE system. Results indicate a significant increasing trend in FP (2000–2020), contrasting with the unimodal (increase-then-decline) trajectories of HQ and WY. Pronounced trade-offs were identified between HQ and WY, and between HQ and FP. Topographic and vegetative factors predominated in shaping the spatial patterns of HQ and FP, whereas climatic factors dictated WY distribution. Specifically, HQ declined when NDVI fell below 0.87, population density surpassed 0.01, or slope was gentler than 7°. WY was constrained when precipitation dropped below 947 mm, actual evapotranspiration exceeded 752 mm, or temperature ranged between 12.5–16.2 °C. FP was suppressed under conditions of slopes > 7°, NDVI within 0–0.61 or 0.61–0.86, or DEM > 373 m. These findings underscore the necessity of spatially explicit management strategies grounded in spatial heterogeneity. We advocate for a multi-objective governance framework centered on HQ to harmonize production and ecological functions. Our findings provide critical insights for formulating policies aimed at sustainably managing protected areas facing similar ecological-production conflicts.