In low permeability reservoirs, CO2 flooding usually leads to gas channeling, whereby a significant amount of CO2 bypasses the oil-bearing formation and fails to effectively displace oil. Introducing water-alternating-gas (WAG) flooding, utilizing water phase stability-driven processes, serves to suppress gas channeling and enhance oil recovery rates. Implementing WAG flooding, which utilizes water phase stability-driven processes, helps suppress gas channeling and improve oil recovery rates. The timing of implementing WAG flooding is crucial. Initiating WAG flooding prematurely can limit the efficiency of CO2 displacement, while initiating it with delays may result in severe gas channeling, resulting in decreased production and increased environmental risks. Finding the balance point is the challenge. The balance point can effectively control gas channeling without reducing the efficiency of CO2 flooding. In this paper, the timing of WAG flooding in low permeability reservoirs is studied in detail. Firstly, this study conducted experimental research to investigate the CO2 displacement process in both homogeneous and heterogeneous cores. Furthermore, it validated the correlation between the timing of WAG injection and the heterogeneity of the cores. The experimental results indicated the existence of an optimal timing for WAG injection, which is correlated with the degree of heterogeneity. Numerical simulation studies were performed to simulate the characteristics of the light oil–CO2 system using the Peng–Robinson (PR) equation. Furthermore, a history matching analysis was performed to validate the experimental results and investigate the correlation between WAG injection and the degree of heterogeneity. The study concluded that as the degree of heterogeneity increases, initiating WAG injection earlier leads to a more significant suppression of gas channeling, increased water–gas interaction, improved gas–oil contact, and enhanced the synergistic effect of increasing the resistance and pressure of WAG flooding and controlling gas channeling. This finding has significant practical implications, as the optimization of WAG injection timing can enhance oilfield production efficiency.