Turbulent flow mixing is essential in optimizing microalgal cultivation in raceway ponds. Microalgal cells are however highly sensitive to hydrodynamic stresses produced by turbulent mixing because of their small size. The mechanical properties (wall deformation and von Misses stress) of the microalgal cell wall structure under the influence of turbulent mixing are yet to be explored. High turbulence magnitudes damage microalgal cell walls by adversely affecting their mechanical properties which consequently destroy the microalgal cells and reduce the biofuel production. Therefore, such a study is required to improve the biofuel productivity of microalgal cells before their cell wall damage in raceway pond. This study developed a novel fluid–structure interaction (FSI)-based numerical model to investigate the effects of turbulent mixing on the cell wall damage of microalgal cells in raceway ponds. The study investigated microalgal cell wall damage at four different locations in a raceway pond in consideration of the effects of pond’s hydrodynamic and geometric properties. An experiment was conducted with a laboratory-scale raceway pond to compare and validate the numerical results by using time-dependent water velocities. Microalgal cell wall shear stress, cell wall deformation, and von Misses stress in the raceway pond were investigated by considering the effects of aspect ratios, water depths, and paddle wheel rotational speeds. Results showed that the proposed numerical model can be used as a prerequisite method for the selection of appropriate turbulent mixing. Microalgal cell wall damage is high in shallow and narrow raceway ponds with high paddle rotational speeds.