To improve loading efficiency and extend the release of carvacrol (Car) for prolonged food preservation, a nanocarrier (NP2) was developed with an encapsulated layer by surface modification of modified HNT (NP1) through silica hydroxylation with chitosan (CS). The study revealed that the tubular structure of the nanotube remained intact post-etching treatment, resulting in a loading efficiency of Car up to 32%, which was 4.6 times higher than untreated HNT. Subsequently, NP2 was successfully prepared and maintained stable loading efficiency. To further understand the loading mechanism of Car by HNT, molecular modeling was utilized to examine the molecular-level interactions, specifically focusing on the hydrogen bonds formed by hydroxyl groups. The resulting nanocomposites (NP2-Car) displayed UV and thermal protection properties. By incorporating NP2-Car into a CS matrix, an active film (CS/NP2-Car) with effective slow-release and antimicrobial capabilities was created, demonstrating its potential for food preservation applications.