Understanding individual differences in brain function is an essential aim of neuroscience. Naturalistic imaging links neural activity to real-life contexts and reflects individual differences in brain response. These unique features make it a promising tool for individualized psychiatry. An essential prerequisite for the extensive use of this paradigm is the reliable representation of inter-individual relationships. We used a test-retest approach to examine whether the naturalistic paradigm reliably represents inter-individual differences, which brain regions have the superior capability, and whether the ability alters with the contents of the stimuli. We quantified the reliability of the inter-subject relationships in repeated scans of two movie clips: a natural sight view and an emotion-evoking story. Besides statistical inference, we included resting-state scans, behavioral tests, and questionnaires as references for the comparison. The results showed that over one-third area of the brain could reliably characterize the inter-individual relationship, and the superior temporal lobe demonstrated comparable reliability representation with the State and Trait Anxiety Inventory. Furthermore, the temporal lobe regions could retain this capability across emotional movies with different contents. This study provides a base for pushing the naturalistic imaging paradigm towards clinical applications and proposes reliable target brain regions for future studies.