Abstract: Ionospheric vertical sounding is a key technology for understanding the space environment and supporting engineering applications such as HF wireless communication and radar. Influenced by the geomagnetic field, the sounding signal splits into ordinary (O) and extraordinary (X) waves as it propagates through the ionosphere. Accurate separation of these two wave modes is a prerequisite for enhancing the application value of ionospheric sounding data. However, O/X wave separation is highly challenging due to the complex electromagnetic environment in the high-frequency band, the time-varying, dispersive, and dissipative nature of the ionosphere, as well as technical limitations of the detection equipment itself. This paper proposes an O/X wave separation method based on polarization matched filtering. By fully exploiting the differences in polarization characteristics between O and X waves and constructing matched filters, high-precision separation of the two waves is effectively achieved. Experimental results show that, after polarization matched filtering of the original sounding data, the suppression ratio for orthogonal polarization can reach 80–140 dB. Compared with existing methods, the proposed approach demonstrates significant advantages in separating O/X waves across ionograms of varying morphologies. This method achieves O/X wave separation from the perspective of polarization signal processing, preserves the original polarization characteristics of the detected O/X waves, and carries clear physical significance. It provides a novel approach for modal analytical separation and offers valuable reference for polarization information processing in other applications.