Two-dimensional transition metal dichalcogenide van der Waals heterojunctions have attracted tremendous attention owing to their superior electronic and optoelectronic properties which can vary depending on their crystal structures. In this work, we investigate the tunable energy band alignments of the phase-engineered 1T’-, hybrid 1T’/2H-, and 2H-phase molybdenum disulfide (MoS2) monolayers measured by X-ray photoelectron spectroscopy and ultraviolet photoelectron spectroscopy. The optical property of the phase-engineered MoS2 monolayer is confirmed by Raman spectroscopy and UV–vis spectrophotometry, and the effects of phase engineering on the band structure and band bending of the heterojunction are investigated. Based on the experimental results, the valence band offset greatly decreases from 5.06 ± 0.1 to 3.93 ± 0.1 eV as the phase transition of MoS2 from 1T’- to 2H-phase occurs, whereas its conduction band offset is reduced and then saturated, attributed to the increased 2H-phase contents causing the broadened bandgaps of the MoS2 monolayer, which is consistent with the results based on Anderson’s rule. Thus, this work provides essential information on the tunable band structure of the phase-engineered MoS2 monolayer that can be optimized depending on the target devices and opens a window for the phase-engineered MoS2 monolayer as a building block for high-performance optoelectronic applications.