This study numerically investigates the interaction between two side-by-side free-falling spheres in water. The predicted S-curve falling trajectories of the spheres were verified by laboratory experiments, and the attraction-repulsion of lateral force on the vertically falling spheres is investigated to give a better understanding of the evolution of the lateral force by excluding the effect of the transverse motion. The flow pattern around the spheres reveals that the wake flows play an essential role in the fluid-sphere interaction. Then, the two free-falling spheres with transverse motion are considered to examine the interacting force and the crosswise strength of wake flows. This study attempts to explore the wake flow as the possible mechanism for the S-curve falling trajectories of two spheres. Finally, the falling processes of the two spheres are simulated in a deeper tank to inspect the falling trajectories and the reappearing flow characteristics.