Defect engineering of van der Waals semiconductors has been demonstrated as an effective approach to manipulate the structural and functional characteristics toward dynamic device controls, yet correlations between physical properties with defect evolution remain underexplored. Using proton irradiation, we observe an enhanced exciton-to-trion conversion of the atomically thin WS2. The altered excitonic states are closely correlated with nanopore induced atomic displacement, W nanoclusters, and zigzag edge terminations, verified by scanning transmission electron microscopy, photoluminescence, and Raman spectroscopy. Density functional theory calculation suggests that nanopores facilitate formation of in-gap states that act as sinks for free electrons to couple with excitons. The ion energy loss simulation predicts a dominating electron ionization effect upon proton irradiation, providing further evidence on band perturbations and nanopore formation without destroying the overall crystallinity. This study provides a route in tuning the excitonic properties of van der Waals semiconductors using an irradiation-based defect engineering approach.