Terahertz metasurface sensors attract extensive attention for excellent characterisics. However, most existing sensing schemes overlooked the polarization state of electromagnetic waves. Here, we propose a plasmonic metasurface sensor based on the elliptical polarization state of reflected EM wave, which can be used for the sensing of influenza A virus. The sensor achieves the conversion from linear polarization to circular polarization within 1–3 THz. By analysing the electromagnetic field distributions of the resonances at 1.43 THz and 2.16 THz, it can be concluded that the polarization conversion originates from the magnetic dipole. Besides, the sensor can characterize the changes in the complex refractive index of the test sample based on the elliptical polarization state of the reflected wave. The electromagnetic response of the metasurface sensor shows an excellent linear relationship between the rotating direction angle of polarization ellipse and the extinction coefficient (k) of the complex RI of the analyte. Furthermore, we also demonstrate the feasibility of detecting three subtypes of Influenza A viruses (H1N1, H5N2, and H9N2) at 1.39 THz though the elliptical polarization state. This sensing approach does not rely on high-precision broadband scanning, providing an alternative perspective for THz biosensing.