The potential risk of airborne cross-infection in multi-compartment dental clinics (MCDCs) requires significant attention. Ventilation systems are crucial for preventing airborne pathogens, but the data available for MCDCs are still inadequate. Therefore, this study evaluated the ventilation performance under different ventilation strategies in an MCDC, including different ventilation modes, the relative positions of ventilation openings and the patient treatment zone, and air changes per hour (ACH). Four aspects of airflow distribution, bioaerosol diffusion (deposition/escape rate and removal index (CRE)), relative exposure index (EP), and fallow time were focused. Ultrasonic scaling experimental data validated the accuracy of the numerical model. The results showed that the DSUR (Down-Supply Up-Return) mode exhibited the best ventilation performance, while the USDR (Up-Supply Down-Return) mode performed poorly due to airflow short-circuiting. In the USUR (Up-Supply Up-Return) mode, the relative positioning of ventilation openings and the patient treatment zone should ensure airflow aligns more consistently with the bioaerosol release direction, promoting quick bioaerosol transport to the outlet as the ACH increases. This boosted the CRE from 0.85 to 1.43 and reduced surface deposition. While the EP decreased significantly within 30 min post-treatment, an 18-min fallow time remained necessary in the DSUR mode. Bioaerosol control in the DSUR mode at 6 ACH matched or exceeded that of other modes at 12 ACH, demonstrating that optimizing the ventilation mode was more effective for creating a safe environment than simply increasing the ventilation rate. These findings can provide a reference for the ventilation design of MCDCs, promoting a healthier dental care environment.