In order to overcome the challenge of lacking polarization encoding in integrated quantum photonic circuits, we propose a scheme to realize arbitrary polarization manipulation of a single photon by integrating a single quantum emitter in a photonic waveguide. In our scheme, one transition path of the three-level emitter is designed to simultaneously couple with two orthogonal polarization degenerate modes in the waveguide with adjustable coupling strengths, and the other transition path of the three-level emitter is driven by an external coherent field. The proposed polarization converter has several advantages, including arbitrary polarization conversion for any input polarization, tunable working frequency, excellent antidissipation ability with high-conversion efficiency, and atomic-scale size. Our Letter provides an effective solution to enable the polarization encoding of photons that can be applied in the integrated quantum photonic circuits, and will boost quantum photonic chips.