Since 2010 the electromagnetic endcap calorimeter based on BGO crystals is used in experiments as one of the systems of the CMD-3 detector. The spacial resolution is one of crucial parameters of the calorimeter. Inaccurate knowledge of the real calorimeter position can limit the resolution. In this work the alignment of the center of the calorimeter with respect to the tracking system of the CMD-3 detector has been performed using events of two-quantum annihilation. The alignment technique that has been used to determine the position of the calorimeter is described. Finally, the improvement in spacial resolution of the calorimeter after applying the correction for the real calorimeter position is shown.