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The Gram–Schmidt orthogonalization procedure (GSOP) and Löwdin symmetric orthogonalization procedure (SYOP) are the two mainstream algorithms for the compensation of phase mismatch in an imperfect optical 90° hybrid. In this paper, we put forward an algorithm switching orthogonalization procedure (ASOP) according to the quality of in-phase and quadrature signals based on the Q value of the eye diagram with less computation. If the quality of the in-phase and quadrature signals has a significant difference, we use the GSOP and select the signal branch with better quality as the initial reference vector for orthogonalization. If they are of about the same quality, then we use the SYOP. We present computer simulations for a coherent free-space optical (FSO) quadrature phase-shift keying (QPSK) communication system and demonstrate the system improvement that can be achieved using the ASOP. Finally, we also show that the proposed ASOP scheme can contribute to the frequency offset and phase estimation of the FSO system in the environment of atmospheric turbulence.