The capability of controlling the phase of the nonlinear polarization of media is vital for nonlinear optical beam shaping. Achieving this control over nonlinear phase manipulation on the nanoscale facilitates modern on-chip photonic integration of nonlinear beam shaping. Plasmonic metasurfaces with thickness down to tens of nanometers can be used to provide the continuous local phases of the nonlinear polarization via the spin-rotation coupling of light, but they still suffer from low conversion efficiency and high absorption loss. Concomitantly, the thickness of dielectric metasurfaces cannot be brought down to a scale lower than hundreds of nanometers. In that context, transition metal dichalcogenide (TMD) monolayers with atomic thickness are known to have high nonlinear conversion efficiency. With that hindsight, here we explain how to manipulate the local phase of the nonlinear polarization from the rotated WS2 monolayer crystals. To verify the theoretical prediction, we also experimentally demonstrate the nonlinear generation of Hermite-Gaussian beams at second-harmonic frequencies via the binary phase manipulation on the patterned WS2 monolayer crystals. Moreover, the deterministic control over the polarization state of the generated nonlinear beam is demonstrated due to the crystal symmetry properties of the TMD monolayer. Our results not only provide a further understanding of light-matter interactions on the atomic scale but also pave the way toward the integration of atomically thin TMD devices into future photonic circuits for optical communication, quantum memory, and computing devices.