Enhanced oil recovery using nanoparticles is a promising method. However, when injected into a reservoir, nanoparticles can block pores and cause permeability damage. Therefore, enhancing their performance to lower the permeability damage effect is crucial. This study investigated the effect of pH alteration through carbon dioxide (CO2) injection on the permeability damage of limestone caused by the aluminum oxide (α-Al2O3) nanofluid. The methodology involved nanofluid alternating CO2 core flooding experiments by using nanofluids with pH of 4.5 and 2.8. After core flooding, permeability damage was calculated as a percentage of the reduction of the original permeability. The results revealed that the permeability damage in the case of nanofluid alternating CO2 injection was 23.23%. In only nanofluid with a pH of 4.5 injection case, permeability damage was 47.53%. In the 2.8 pH nanofluid injection case, permeability damage was 31.01%. The retention of nanoparticles was confirmed through scanning electron microscopy and energy dispersive X-ray analysis. Permeability damage could be attributed to a large nanoparticles’ agglomeration size, roughness of pore surfaces, and nanoparticle sedimentation. The results of the study revealed that altering pH through the α-Al2O3 nanofluid alternating CO2 injection can effectively reduce the permeability damage of limestone.