This study compared the demineralization resistance of teeth treated with silver diamine fluoride (SDF) to that treated with fluoride varnish. A total of 105 healthy bovine incisors were divided into control, fluoride varnish, and SDF groups. The enamel surface density change was then measured by micro-computed tomography (micro-CT) at three depths. The demineralized zone volume was measured on 3D micro-CT images to evaluate the total demineralization rate. The enamel surface morphology was assessed by scanning electron microscope. The enamel density had continuously decreased while demineralization increased in the control and fluoride varnish groups. The enamel density had increased in the SDF group till the 7th day of demineralization treatment and decreased thereafter. However, the decrease in the SDF group was less severe than that in the other groups (p < 0.05). The demineralized enamel volume had increased through treatment and was the highest in the control group, followed by the fluoride varnish and SDF group. The enamel surface morphology was the roughest and most irregular in the control group, followed by the fluoride varnish group and SDF groups.