This paper presents findings from indoor physical simulation experiments using a tandem core model to simulate and examine the water intrusion patterns in carbonate reservoirs under non-homogeneous conditions. This study analyzed the characteristics of the side-bottom water and gas flow as well as the mechanism of water control following the CO2 injection by changing the time and amount of gas injection. The results indicated that the side-bottom water intrusion can be divided into four phases: the injection of CO2 can inhibit the water intrusion and the mechanism of the CO2 injection. The experimental results showed that the water intrusion in the tandem core model can be divided into four stages: slow seepage of side water, stable seepage of side water, seeing water, and complete flooding. The results from CO2 injection under different conditions suggest that the optimal interval for gas injection volume to control water effectively should be no less than 66%, with an anticipated increase in the recovery rate of around 21.6%–26.6%. The optimal interval for CO2 injection to control water should be no less than 66%, with an increase in the recovery rate of about 21.6%–26.6%. The optimum interval for CO2 injection to control water should be no less than 66%. The injection of CO2 water during complete flooding has the potential to extend the production cycle of the gas well.