Two-dimensional materials (2DMS) have emerged as key potential materials for electronic, spintronics, photocatalytic, and energy storage device applications, due to their outstanding intrinsic properties. Additionally, ion irradiation, a technique in which energetic beams of charged particles are exposed on materials, enhances the formation of atomic defects toward changing the materials' properties significantly even for superior performances over their conventional counterparts. Monolayer MoS2 has shown several potential applications as semiconductor with an intrinsic direct band gap. In this study, we have grown monolayer MoS2 on sapphire substrate via. thermal chemical vapor deposition approach and homogenously irradiated with 100 keV helium ions (1 × 1013–1 × 1016 ions cm−2 fluence) and argon ions (1 × 1013–1 × 1014 ions cm−2 fluence) at room temperature to study the effects of ion beam irradiation specifically on surface morphology, structure, optical, and chemical compositions. Both the micro-Raman and photoluminescence studies confirmed the sequential reduction in sulfur atomic concentration due to preferential sputtering and infusion of associated defects, which provide additional nucleation sites due to sulfur vacancies. Consequently, we observed evolutions of MoS2 nano-island on monolayer MoS2 edges due to well controlled low-energy ion irradiation. The study not only leveraging the better understanding and gain of knowledge on the effects of low-energy ion exposers on monolayer MoS2 but also opening a gateway for generating MoS2 nanostructures having potential applications in 2D electronics, spintronics (once integrated with magnetic impurities), and photocatalytic applications.