As the most potential renewable biomass energy, microalgae has significant advantages in the fields of biological carbon sequestration and biofuel production, which contributes to the realization of carbon peak and carbon neutrality goals. The cultivation efficiency of microalgae can be greatly improved by improving the performance of the aeration device of the reactor. In this work, the spherical aeration structure of the columnar photobioreactor was optimized by numerical simulation. The Euler model and k?ε model were used for the simulation and turbulence model, respectively. The changes of gas holdup, liquid velocity, turbulent kinetic energy, and the flow field in the photobioreactor under different aeration conditions were studied and analyzed. The results showed that the change in the structure of the aeration device had a great impact on the flow characteristics in the photobioreactor. When the aeration device was aerated into the reactor, the gas holdup, liquid velocity, and turbulent kinetic energy increased with the increase of the aeration rate and decreased with the increase of the aeration pore size. According to all relevant parameters, when the total aeration rate was 1400 mL/min, the number of aeration pores was 50, and the aeration pore size was 30 μm, the aerator had the best performance. At this time, the measured gas holdup was 68.6%, the liquid velocity was 0.905 m/s, and the turbulent kinetic energy was 0.149 m2/s2. The numerical simulation provided an effective way to optimize the aeration structure parameters, which benefited the photobioreactor design for microalgae cultivation and sewage treatment associated with CO2 fixation.