Two-dimensional materials and ionic liquids are widely used as lubricating materials due to their excellent tribological properties. This study designed three water-based proton-ionic liquids (PILs) and synthesized molybdenum disulfide (MoS2) nanosheets for their combination as water-based lubricant additives. The composite lubrication system exhibits excellent tribological properties, with a friction coefficient as low as 0.024, reducing friction by 90.77% compared to water–glycol. Mechanism studies have shown that the excellent lubrication performance comes from the adsorption of ionic liquids at sliding interfaces, the interlayer slip of MoS2, and the generation of tribofilms at wear scars. This work provides theoretical support and technical guidance for the design and preparation of new water-based lubricating additives.