In this contribution, we use heavy ion irradiation and photoluminescence (PL) spectroscopy to demonstrate that defects can be used to tailor the optical properties of two-dimensional molybdenum disulfide (MoS2). Sonicated MoS2 flakes were deposited onto Si/SiO2 substrate and subjected to 3 MeV Au2+ ion irradiation at room temperature to fluences ranging from 1 × 1012 to 1 × 1016 cm−2. We demonstrate that irradiation-induced defects can control optical excitations in the inner core shell of MoS2 by binding A1s- and B1s-excitons, and correlate the exciton peaks to the specific defects introduced with irradiation. The systematic increase of ion fluence produced different defect densities in MoS2, which were estimated using B/A exciton ratios and progressively increased with ion fluence. We show that up to the fluences of 1 × 1014 cm−2, the MoS2 lattice remains crystalline and defect densities can be controlled, whereas at higher fluences (≥1 × 1015 cm−2), the large number of introduced defects distorts the excitonic structure of the material. In addition to controlling excitons, defects were used to split bound and free trions, and we demonstrate that at higher fluences (1 × 1015 cm−2), both free and bound trions can be observed in the same PL spectrum. Most importantly, the lifetimes of these states exceed trion and exciton lifetimes in pristine MoS2, and PL spectra of irradiated MoS2 remains unchanged weeks after irradiation experiments. Thus, this work demonstrated the feasibility of engineering novel optical behaviors in low-dimensional materials using heavy ion irradiation. The insights gained from this study will aid in understanding the many-body interactions in low-dimensional materials and may ultimately be used to develop novel materials for optoelectronic applications.