Photoemission orbital tomography (POT) from photoelectron momentum maps (PMMs) has enabled detailed analysis of the shape and energy of molecular orbitals in the adsorbed state. This study proposes a new POT method based on the PhaseLift. Molecular orbitals, including three-dimensional phases, can be identified from a single PMM by actively providing atomic positions and basis. Moreover, our method is robust to noise and can perfectly discriminate adsorption-induced molecular deformations with an accuracy of 0.05 [angstrom]. Our new method enables simultaneous analysis of the three-dimensional shapes of molecules and molecular orbitals and thus paves the way for advanced quantum-mechanical interpretation of adsorption-induced electronic state changes and photo-excited inter-molecular interactions.