Ion irradiation is a versatile and convenient tool for modifying the optical, electrical, and catalytic properties of two-dimensional (2D) materials through controlled induction of impurities and defects. The behavior of 2D materials under ion irradiation is interesting, which needs to be explored in the contest of their optoelectronic applications. In the present work, we have reported the effect of H+-ion irradiation on layered α-MoO3 flakes by defect engineering. Initially, the α-MoO3 crystals were synthesized using the physical vapor deposition technique followed by mechanical exfoliation of an as-grown crystal to obtain α-MoO3 flakes of different thicknesses. Then, the exfoliated flakes were exposed to H+-ion/proton irradiation with a fluence of 1 × 1016 ions/cm2 using a 30 keV source. After irradiation, new photoluminescence (PL) emission peaks were observed at different positions in the range of ∼2.4–1.9 eV, which was found to be absent in pristine flakes. Raman studies revealed non-uniform oxygen vacancy distribution in H+-ion irradiated α-MoO3 flakes, which affected the PL peak positions. Additionally, first-principle calculations and Bader charge analysis were performed to identify the origin of the new PL peaks. Our findings indicate that oxygen vacancies positioning at different locations of the α-MoO3 lead to the emergence of new absorption peaks within the range of ∼2.2–1.25 eV, which is consistent with our experimental findings. The present study gives insight into exploring the use of ion-irradiated α-MoO3 in optoelectronics applications with tunable properties.