In order to improve the anti-interference performance of sea surface target detection, based on polarization filtering technology, a polarization characteristic estimation and suppression method of sea surface flare was designed, and a polarization two-way reflection distribution model was established based on the GGX model, and different wind speeds and different detection azimuth differences were simulated and analyzed. The results show that there is no significant change in flare characteristics at different wind speeds. The detection azimuth difference is 180° in the main reflective surface, the flare phenomenon is obvious, and the polarization angle is in the range of 90~95°. Finally, the method in this paper is applied to a certain type of optoelectronic equipment, and the sea surface verification test is carried out for the practical application scenario in a sea area of Dalian. The experimental results show that the flare suppression effect is the best when the polarization angle is 90°, the contrast of the best image is increased by 21.26% on average, and the proportion of saturated pixels is reduced by 84.48% on average. Compared with the detection results of traditional optoelectronic equipment, the polarization method can effectively suppress the sea surface flare interference and improve the detection performance of the target under the sea surface flare interference.