Reconfigurable metasurfaces have shown unprecedented capabilities in controlling electromagnetic (EM) waves in recent years and play an essential role in information manipulation. However, most research on reconfigurable metasurfaces is limited to planar rigid structures, with only one control function and suitable for specific single polarization. Achieving simultaneous control of phase, polarization, and frequency in the conformal structure has significant practical implications in many applications, but remains obviously challenging. In this paper, a flexible multifunctional time‐varying phase‐modulated metasurface (MTPM) with orthogonal polarization control is proposed for conformal applications to manipulate the spectrum distribution. It enables time encoding capability in controlling the phase characteristics of x‐ and y‐polarized EM waves individually by switching the bias voltage of the PIN diode in two directions. Discrete harmonic spectrum and continuous Doppler frequency shifts are implemented separately on two orthogonal polarizations by applying different time coding sequences. As a practical application, a conformal MTPM for radar feature transformation is explored. Multiple discrete false targets and defocusing phenomena can be realized respectively for x‐ and y‐polarized waves. Both simulated and measured results verify the validity of the proposed method and prototype.