Neurovascular coupling (NVC) underpins the interpretation of hemodynamic signals as proxies for neural activity, yet its response to metabolic perturbations remains poorly understood. Here, we leverage concurrent fluorescence calcium imaging and functional magnetic resonance imaging in mice expressing genetically encoded calcium indicators to dissect how elevated CO₂ levels reshape the interplay between neural and vascular responses. Our findings indicate that hypercapnia induces opposing trends in calcium and blood-oxygen-level-dependent (BOLD) responses, accompanied by global desynchronization of brain activity. Additionally, 5% CO₂ suppressed sensory-evoked BOLD and hemoglobin responses, while neuronal and astrocytic activity remained unaffected. Dynamic functional connectivity and co-activation pattern analyses further reveal a dissociation in the coordination between BOLD hemodynamic responses and their underlying neural dynamics under hypercapnic conditions. Notably, we observed that hemodynamic responses, normally driven by neuronal signaling, get attenuated with BOLD signals no longer reflecting neural activity patterns in the brain. These findings demonstrate that hypercapnia can override conventional NVC relationships, compelling a reassessment of how BOLD contrast is interpreted under hypercapnic stress in preclinical and clinical settings. This holds particular relevance for chronic hypercapnia-related conditions where a deeper understanding of NVC disruption may inform improved diagnostic and therapeutic strategies.