The development of nonprecious electrochemical catalysts for water splitting is a key step to achieve a sustainable energy supply for the future. Molybdenum disulfide (MoS2) has been extensively studied as a promising low‐cost catalyst for hydrogen evolution reaction (HER), whereas HER is only catalyzed at the edge for pristine MoS2, leaving a large area of basal plane useless. Herein, on‐surface self‐assembly is demonstrated to be an effective, facile, and damage‐free method to take full advantage of the large ratio surface of MoS2 for HER by using multiscale simulations. It is found that as supplement of edge sites of MoS2, on‐MoS2 M(abt)2 (M = Ni, Co; abt = 2‐aminobenzenethiolate) owns high HER activity, and the self‐assembled M(abt)2 monolayers on MoS2 can be obtained through a simple liquid‐deposition method. More importantly, on‐surface self‐assembly provides potential application for overall water splitting once the self‐assembled systems prove to be of both HER and oxygen evolution reaction activities, for example, on‐MoS2 Co(abt)2. This work opens up a new and promising avenue (on‐surface self‐assembly) toward the full exploitation of the basal plane of MoS2 for HER and the preparation of bifunctional catalysts for overall water splitting.