The incompatibility between workover fluid and reservoir rock is one of the causes of formation damage. Fines migration and clay swelling are considered as the major mechanisms responsible for formation damage, which results in declining productivity. However, there has been limited visualized evidence of pore structural changes during formation damage. This paper establishes a formation damage evaluation method for sandstone reservoirs based on X-ray micro-computed tomography (CT) analysis. We presented conclusive evidence for clay swelling and fines migration during workover fluid flooding and formation liquid flooding. Water sensitivity and flow rate sensitivity tests were performed on a Dongying sandstone (heterogeneous argillaceous sandstone) plug. In addition, the plug was micro-CT imaged before and after flooding with workover fluid and formation liquid at medium resolution (24 μm voxel size); the changes in core permeability and the associated changes in 2D and 3D pore space were analyzed. We found that the sandstone pore space was partially blocked by clay minerals and moving particles, leading to significantly decreased porosity (5.17%–4.19% for sample 1, 5.38%–2.76% for sample 2) and permeability (3.38 × 10−3 μm2 to 1.28 × 10−3 μm2 for sample 1, 13.30 × 10−3 μm2 to 3.15 × 10−3 μm2 for sample 2). This permeability decrease was caused by a decrease in the average pore radius and coordination number. Moreover, increased micro-CT intensity was measured by comparison of initial and final tomogram images, representing clay swelling & blockage of pores during the displacement and a generally lower porosity. This work visualized microscale formation damage, which reminds that incompatibility between workover fluid and reservoir rock damages formation seriously and the fluid injection rate should be lower than the critical flow rate when developing a reservoir with a strong water sensitivity and flow rate sensitivity.