Semiconducting heterojunctions (HJs), comprised of atomically thin transition metal dichalcogenides (TMDs), have shown great potentials in electronic and optoelectronic applications. Organic/TMD hybrid bilayers hold enhanced pumping efficiency of interfacial excitons, tunable electronic structures and optical properties, and other superior advantages to these inorganic HJs. Here, we report a direct probe of the interfacial electronic structures of a crystalline monolayer (ML) perylene-3, 4, 9, 10-tetracarboxylic-dianhydride (PTCDA)/ML-WSe₂ HJ using scanning tunneling microscopy, photoluminescence, and first-principle calculations. Strong PTCDA/WSe₂ interfacial interactions lead to appreciable hybridization of the WSe₂ conduction band with PTCDA unoccupied states, accompanying with a significant amount of PTCDA-to-WSe₂ charge transfer (by 0.06 e/PTCDA). A type-Ⅱ band alignment was directly determined with a valence band offset of ~ 1.69 eV, and an apparent conduction band offset of ~ 1.57 eV. Moreover, we found that the local stacking geometry at the HJ interface differentiates the hybridized interfacial states.