This study deals with the hybrid wind tunnel which combines wind tunnel experiment and numerical simulation to obtain the exact and detailed information of real flows. The hybrid wind tunnel based on the observer theory utilizes partial information of the real flow from pressure measurement for the numerical simulation through a feedback loop to overcome the difficulty of specifying exact boundary or initial conditions as well as the effect of modeling error. In previous two-dimensional analyses on the hybrid wind tunnel, the difference between computation and experiment in regard to perturbation velocity increased with the computational grid of a high resolution due to the inappropriateness of the two-dimensional model. In this paper, three-dimensional analyses with three grid systems of different resolutions are performed on the hybrid wind tunnel for a fundamental flow with the Karman vortex street behind a square cylinder. The reproducibility of a velocity field on the hybrid wind tunnel is improved in three-dimensional analysis by using the high resolution grid system. In addition, three-dimensional analysis with the coarse grid system on the hybrid wind tunnel effectively reduces the error due to the insufficient grid resolution for ordinary numerical simulation.