Oscillatory baffled reactors (OBRs) have attracted much attention from researchers and industries alike due to their proven advantages in mixing, scale-up, and cost-effectiveness over conventional stirred tank reactors (STRs). This study quantitatively investigated how different mixing indices describe the mixing performance of a moving baffle OBR using computational fluid dynamics (CFD). In addition, the hydrodynamic behavior of the reactor was studied, considering parameters such as the Q-criterion, shear strain rate, and velocity vector. A modification of the Q-criterion showed advantages over the original Q-criterion in determination of the vortices’ locations. The dynamic mesh tool was utilized to simulate the moving baffles through ANSYS/Fluent. The mixing indices studied were the velocity ratio, turbulent length scale, turbulent time scale, mixing time, and axial dispersion coefficient. We found that the oscillation amplitude had the most significant impact on these indices. In contrast, the oscillatory Reynolds number did not necessarily describe the mixing intensity of a system. Of the tested indices, the axial dispersion coefficient showed advantages over the other indices for quantifying the mixing performance of a moving baffle OBR.