Dissipation dilution has driven a revolution in the quality factors (Q) of top-down nanomechanical resonators. Yet it has not been leveraged for van der Waals (vdW) materials. Here we report quality factors up to 372,000±37,000 in monolayer MoS₂ drums at 4 K, nearly an order of magnitude beyond the previous best for any vdW material at this temperature, enabled by a clean, polymer-free exfoliation technique. We develop a dissipation-dilution model for circular drums and analyze the contributing intrinsic and extrinsic dissipation mechanisms. The MoS₂ monolayer exhibits a dilution factor of order 1,000, establishing sub-nanometer-thin resonators as ultimate dilution materials. The intrinsic quality factor, however, is limited by surface losses at atomic thickness. Conversely, multilayer drums show a lower dilution factor but a high intrinsic quality factor, on par with established top-down materials of similar dimensions, both resulting from the increased thickness. A two-level-system analysis of the temperature-dependent damping confirms this bulk-versus-surface picture and provides first insight into its microscopic origin. Our results identify dissipation dilution as the governing mechanism for high-Q mechanical vdW resonators. Combined with strategies such as soft clamping or stress engineering, they establish atomically thin resonators as a platform for ultrahigh-Q quantum transduction and sensing.