Background: Integrating electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) with naturalistic stimuli has advanced our understanding of the neural mechanisms underlying mental disorders. Naturalistic paradigms use dynamic, multimodal stimuli that capture complex emotional and cognitive processes more effectively than traditional experimental designs. Objective: This review synthesizes research from 2014 to 2024 exploring neural mechanisms of anxiety, depression, and schizophrenia within naturalistic paradigms. Methods: Recent EEG-fMRI studies employing naturalistic tasks were examined to identify common and disorder-specific neural alterations across affective and cognitive networks. Results: In anxiety, hyperactivity in the amygdala, prefrontal cortex, anterior cingulate cortex, and insula, together with changes in the dorsal attention, default mode, and frontoparietal networks, reflects excessive fear responses and impaired regulation. Depression is characterized by disruptions in default mode and frontoparietal connectivity and altered amygdala-prefrontal interactions, indicating maladaptive introspection and cognitive control. Schizophrenia shows abnormalities in motor and language processing, with aberrant activity in frontal, parietal, and temporal regions including the insula and temporoparietal junction. Conclusion: These findings highlight the shared involvement of the amygdala, prefrontal cortex, anterior cingulate cortex, and insula across disorders and demonstrate the potential of naturalistic paradigms for advancing personalized diagnostics and interventions in mental health.