The magnetorheological (MR) repair method can effectively repair the small-scale damage of fused silica optics and further improve the laser-induced damage threshold of fused silica optics. However, at present, the rules of MR repair of small-scale damage of fused silica are not clear and cannot provide further guidance for the repair process. In this paper, the fused silica damage samples were repaired layer by layer by the MR method. The number and size changes of all the surface damage, the morphology, the fluorescence area distribution, and photothermal-absorption value of a single typical small-scale damage were measured. Through dark field scattering imaging, it is found that when the repair depth is 5 μm, the repair completion rate of damage with a transverse size less than 50 μm can reach 44%, and the repair efficiency decreases gradually with the repair process. Focusing on the whole repair process of a single typical, small-scale damage—due to the flexible shear removal mechanism of the MR method—the repair process of damage can be divided into three stages, which as a whole is a top-down, from outside to inside process. The first stage is the process of removing the surface of the damage layer by layer. In this process, MR fluid will introduce pollution to the inside of the damage. In the second stage, MR fluid begins to repair the inside of the damage. In the third stage, the MR ribbon completely covers the inside of the damage, and the repair effect is the most obvious. The measurement results of photothermal absorption and fluorescence area distribution of damage confirm this process. The photothermal absorption value and fluorescence area distribution of damage do not simply decrease with the repair process. On the contrary, they gradually increase first, and then decrease significantly when the damage depth reaches less than 1 μm. As the thickness of the MR ribbon is 1 μm, the reduction in the photothermal absorption value and fluorescence area of the damage is due to the process of repairing the inside of the damage. The results show that the absorbent impurities inside the small-scale damage of fused silica are the main factor affecting the performance. The key to repairing the small-scale damage of fused silica by the MR method is that the damaged interior must be repaired effectively. This paper outlines the MR repair method of small-scale damage of fused silica, which is of great significance to optimize the MR repair process.