Background: Dental caries, a prevalent oral disease, has long been a focal point of research in dentistry concerning its prevention and treatment. While hydroxyapatite (HAP) repair coatings and sodium fluoride solutions are commonly employed for combating dental caries, but their effectiveness and underlying mechanisms are not fully understood. This study aims to investigate the preventive impact of hydroxyapatite repair coatings on oral infectious caries in rats. Methods: To create an oral infectious caries model, a total of 35 Wistar rats were selected. After the selection process, 30 rats successfully were established as the model. These rats were randomly divided into three distinct groups for treatment purposes. The first group was the physiological saline group, where the surface of teeth was gently wiped with cotton soaked in physiological saline. The second group was the sodium fluoride group, in which the surface of the teeth was wiped with cotton soaked in sodium fluoride solution. The third group was the experimental group, where the surface of the teeth, previously corroded by acid, was treated with HAP paste. The treatment was performed once a week for a total of four weeks. To evaluate the effectiveness of each treatment, the colony count and Keyes score were recorded. Furthermore, the morphology of the tooth surface for each group was closely observed using an electron microscope. Results: Based on the experimental results, the experimental group showed significant improvement after four weeks of treatment. The colony count revealed a significant decrease in the number of Streptococcus mutans in the experimental group (p < 0.05). Additionally, the Keyes score demonstrated that the experimental group had significantly lower scores in the enamel (E)-level and slight dentinal (Ds)-level on the smooth surface of caries compared to both the sodium fluoride group and the saline group, with statistical significance (p < 0.05). At the moderate dentin (Dm)-level, the experimental groups scores were significantly lower than those of the control group (p < 0.05). The electron microscopy results showed that the experimental group exhibited a marked enhancement in the surface structure of the teeth. Specifically, the experimental group displayed shallow demineralization areas and a reduced number of cavities compared to the sodium fluoride group and the physiological saline group. Furthermore, the experimental group showed a superior ability to inhibit dental caries, indicating its potential as a promising solution for dental health. Conclusions: The application of HAP repair coatings has demonstrated a substantial reduction in the population of Streptococcus mutans within the oral cavity of rats, with no significant difference in the degree of damage on smooth and cracked surfaces of caries compared to the sodium fluoride group. Electron microscopy observations showed that HAP repair coatings can protect the surface of enamel from acid erosion and abrasion. These results suggest the promising potential of HAP restorative coatings in the prevention of dental caries and provide novel directions for future clinical practice.