The quantitative correlation of the catalytic activity with microscopic structure of heterogeneous catalysts is a major challenge for the field of catalysis science. It requests synergistic capabilities to tailor the structure with atomic scale precision and to control the catalytic reaction to proceed through well-defined pathways. Here we leverage on the controlled growth of MoS2 atomically thin films to demonstrate that the catalytic activity of MoS2 for the hydrogen evolution reaction decreases by a factor of ~4.47 for the addition of every one more layer. Similar layer dependence is also found in edge-riched MoS2 pyramid platelets. This layer-dependent electrocatalysis can be correlated to the hopping of electrons in the vertical direction of MoS2 layers over an interlayer potential barrier. Our experimental results suggest the potential barrier to be 0.119V, consistent with theoretical calculations. Different from the conventional wisdom, which thinks that the number of edge sites is important, our results suggest that increasing the hopping efficiency of electrons in the vertical direction is a key for the development of high-efficiency two-dimensional material catalysts.