This research underscores the exceptional potential of Bacillus clausii as a probiotic for food products. Our study assessed Bacillus clausii under simulated gastrointestinal conditions, revealing its impressive resilience: 58% resistance to pepsin, 70% to bile salts and pancreatin, and 41% viability at low pH. It also showed significant auto-aggregation (42.87%) and co-aggregation with Escherichia coli ATCC 35150 (44.6%), Bacillus cereus ATCC 13061 (59.7%), and Staphylococcus aureus ATCC 13150 (30.9%). The strain's antibiotic sensitivity profile—susceptible to ampicillin and vancomycin, resistant to trimethoprim and erythromycin—ensures its safety for food use, confirmed by the absence of hemolysis, gelatinase activity, biogenic amine production, and toxicity in Caenorhabditis elegans. Remarkably, Bacillus clausii exhibited high thermal stability, with survival rates up to 96.31% at 90 °C for 30 min and 82.76% at 100 °C for 60 min, and a broad pH tolerance (41%–99.7% survival from pH 2 to 12). The strain's response to heat stress involved key antimicrobial and spore formation genes (spaS, sboA, BAC A, and SPO). This study establishes Bacillus clausii OHRC1 as a robust, safe, and versatile probiotic, suitable for enhancing food quality and safety in ready-to-eat products.