Monolayer or ultrathin transition metal dichalcogenides cover a wide range of atomically thin two-dimensional (2D) materials, whose fascinating properties have made them promising candidates for many applications. In this work, ultrathin MoS₂ flakes were successfully exfoliated, induced by bovine serum albumin (BSA) or hemoglobin (HB), under vigorous ultra-sonication. They were used as additives for water-based lubricating systems and related investigations indicated that they could improve the friction performance and anti-wear abilities at a relatively low concentration: 0.10 wt% of additive contents can make the average friction coefficient stabilize in the range between 0.06 and 0.08, which results from the formation of a dynamic protective film on the friction surfaces. The protein-induced ultrathin MoS₂ flakes are also expected to be useful for other hydrophilic lubrication systems, which possess great scientific value and promising application prospects compared with bulk or microscale lubricating additives.