Quantum communication is a transmission technology that allows legitimate users to share a secret key. The BB84 protocol employs four linear polarization states for encoding in our quantum key distribution system. However, the optical elements affect the polarization features of quantum state, which leads to errors in decoded key. To reduce mistakes and increase device encoding performance, a polarization controller is included in the optical circuit. An algorithm identifying the angles of the polarization controller's wave plates has been developed. We conclude that using a polarization controller and the method of finding angles has improved the polarization extinction ration for all encoding channels of designed free-space transmitter. Finding angles of the plates is a problem of optimizing the search for parameters where the trace of matrix is maximum in the Stokes-Muller formalism. We used the gradient descent approach to determine the angles of the plates and we were able to obtain optical part of QBER values of 0.12 percent, so decreasing its values by 185 times.