Purpose This study was performed to investigate the effect of exposure parameters on image quality obtained using a cone-beam computed tomography (CBCT) scanner and the relationship between physical factors and clinical image quality depending on the diagnostic task. Materials and Methods CBCT images of a SedentexCT IQ phantom and a real skull phantom were obtained under different combinations of tube voltage and tube current (Alphard 3030 CBCT scanner, 78–90 kVp and 2–8 mA). The images obtained using a SedentexCT IQ phantom were analyzed technically, and the physical factors of image noise, contrast resolution, spatial resolution, and metal artifacts were measured. The images obtained using a real skull phantom were evaluated for each diagnostic task by 6 oral and maxillofacial radiologists, and each setting was classified as acceptable or unacceptable based on those evaluations. A statistical analysis of the relationships of exposure parameters and physical factors with observer scores was conducted. Results For periapical diagnosis and implant planning, the tube current of the acceptable images was significantly higher than that of the unacceptable images. Image noise, the contrast-to-noise ratio (CNR), the line pair chart on the Z axis, and modulation transfer function (MTF) values showed statistically significant differences between the acceptable and unacceptable image groups. The cut-off values obtained using receiver operating characteristic curves for CNR and MTF 10 were useful for determining acceptability. Conclusion Tube current had a major influence on clinical image quality. CNR and MTF 10 were useful physical factors that showed significantly associations with clinical image quality.