In this paper, the gas-liquid flow pattern and CO2 dissolution transport process of microalgae solution in an air-lift photobioreactor (PBR) are investigated by numerical simulations. In order to promote the gas-liquid mass transfer efficiency to enhance the carbon fixation, we propose different optimization schemes for the structure. Firstly, a two-phase flow model and a mass transfer model are employed to investigate the fluid flow characteristics. The flow state is evaluated by velocity in light direction, turbulent kinetic energy (TKE), gas hold-up and CO2 mass transfer coefficient. The results show that the gas flow rate of 0.2 V/V/min is the optimum value for the inlet. Secondly, CO2 mass transfer and carbon fixation rates are analyzed for different inlet CO2 volume fractions. With the increase of CO2 volume fraction, the carbon fixation rate first increases and then decreases, the highest fixation rate reaching 2.21 × 10−4 mol m−3 s−1 at 6 %. Finally, based on numerical simulations, three optimized structures with different spacing of baffles are proposed and evaluated the performance in comparison with the original. The results show that the gas distribution and CO2 mass transfer are significantly improved, with the one-sided baffle structure is the best. In summary, this study provides a new and useful reference to evaluate the gas-liquid mixing and improve the microalgae carbon fixation rate.