Molybdenum disulfide (MoS2) has moderate hydrogen adsorption free energy, making it an excellent alternative to replace noble metals as hydrogen evolution reaction (HER) catalysts. The thickness of MoS2 can affect its energy band structure and interface engineering, which are the avenue way to adjust HER performance. In this work, MoS2 films with different thicknesses were directly grown on the glassy carbon (GC) substrate by atomic layer deposition (ALD). The thickness of the MoS2 films can be precisely controlled by regulating the number of ALD cycles. The prepared MoS2/GC was directly used as the HER catalyst without a binder. The experimental results show that MoS2 with 200-ALD cycles (the thickness of 14.9 nm) has the best HER performance. Excessive thickness of MoS2 films not only lead to the aggregation of dense MoS2 nanosheets, resulting in reduction of active sites, but also lead to the increase of electrical resistance, reducing the electron transfer rate. MoS2 grown layer by layer on the substrate by ALD technology also significantly improves the bonding force between MoS2 and the substrate, showing excellent HER stability.