Despite the passage of approximately five years since the outbreak, an efficacious remedy for SARS-CoV-2 remains elusive, highlighting the urgent imperative for developing SARS-CoV-2 potent inhibitors. In our current study, we have unmasked the hitherto unrealized potential of dihydropyrimidine-2-thiones against the Main Protease (M^pro) of SARS-CoV-2. Employing a predictive docking tool, we identified promising lead compounds and optimized them via comprehensive Structural Activity Relationship (SAR) studies. Key design elements included proton donor/acceptor groups, six-membered rings, and fluorinated moieties to enhance interactions. These leads underwent in vitro inhibition assays to enhance their interaction with key M^pro amino acid residues. Our findings indicated that all synthesized compounds exhibited significant inhibition of the M^pro. Compounds 12j (IC₅₀ = 0.063 μM), and 12l (IC₅₀ = 0.054 μM) displayed exceptional in vitro binding affinities. In addition to their string inhibitory activity, CC₅₀ values were assessed, confirming acceptable cytotoxicity profiles for potent compounds. Molecular dynamic simulation substantiated the binding mechanism revealing that compound 12l maintains robust stability with the target protein. Furthermore, compounds predicted to have minimal oral toxicity and high intestinal absorption make them promising candidates for drug development. These findings paved the way for the potent clinical application of these dihydropyrimidine-2-thiones as efficient SARS-CoV-2 therapeutics.