The relationship between growth rates of algae and structure parameters of closed flat-panel photobioreactors was investigated. Ad/Ar (cross-section area of the downcomer/cross-section area of the riser), h 0 (clearance from the upper edge of the baffles to the water level), and h 1 (clearance from the lower edge of the baffles to the bottom of the reactor) were selected as the inner structure parameters. CFD (Computational Fluid Dynamics) was used to simulate the hydrodynamic parameter (TKE) d (turbulence kinetic energy of the downcomers) and the secondary parameters ε (ratio between td and tc), tc (cycle time), and DZ (dead zones), which were deduced from the hydrodynamic parameters mentioned above. The effects of (TKE) d, ε, tc, DZ, and the inner structure parameters on cell growth of Isochrysis galbana 3011 were analyzed using data collected in 15-L airlift flat-panel photobioreactors. A model was developed to predict algae cell growth based on these inner structure parameters, thereby providing a new method for photobioreactor optimization. Validity of the model was confirmed by experimental data of I. galbana 3011 cultured in 15-L and 300-L photobioreactors, respectively. Finally, the prospect of applying CFD to photobioreactor optimization was discussed.