The polarization modulation of Cherenkov diffraction radiation facilitates intriguing potentials to explore material properties and advanced technologies such as free-electron lasers; however, it is still challenging to achieve polarization modulation. Here, we propose versatile on-chip silicon-patterned silicon-nitride photonic integrated waveguides to produce a direction-dependent polarization modulator for Cherenkov diffraction radiation. The radiation angle can be manipulated arbitrarily by arranging the period of the grating and the propagation direction of the electron beam. Furthermore, the polarization and the number of output directions of the radiation can be controlled by the gradient metasurfaces. In particular, the linear, left-, and right-handed circular polarized Cherenkov diffraction radiation could be generated in separate radiation directions. Our results pave the way to modulate the polarization of free-electron radiation and further promote the development of on-chip light sources.