When the linearly polarized object and reference beams with the same polarization direction are used for recording gratings in bacteriorhodopsin films, the azimuth of polarization of the reconstruction beam has an influence on the diffraction efficiency. By using Jones matrices to analyze this phenomenon, we find that the azimuth of polarization of the reconstruction beam makes a cosine modulation on the diffraction efficiency. The diffracted beam is linearly polarized only when the polarization of the reconstruction beam is parallel or perpendicular to that of the recording beams; otherwise, the diffracted beam becomes elliptically polarized. The azimuth of polarization of the reconstruction beam produces a positive cosine modulation on the peak diffraction efficiency, but a negative cosine modulation on the steady diffraction efficiency (with phase difference π). By adding auxiliary violet light during grating formation, the saturation of the grating can be restrained; as a result, the negative cosine modulation of the steady diffraction efficiency changes to the positive cosine modulation and also the steady diffraction efficiency is increased apparently.