Earth-abundant hydrogen evolution catalysts are essential for high-efficiency solar-driven water splitting. Although a significant amount of studies have been dedicated to the development of new catalytic materials, the microscopic assembly of these materials has not been widely investigated. Here, we describe an approach to control the three-dimensional (3D) assembly of amorphous molybdenum sulfide using polymer brushes as a template. To this end, poly(dimethylaminoethyl methacrylate) brushes were grown from highly oriented pyrolytic graphite. These cationic polymer films bind anionic MoS42– through an anion-exchange reaction. In a final oxidation step, the polymer-bound MoS42– is converted into the amorphous MoSx catalyst. The flexibility of the assembly design allowed systematic optimization of the 3D catalyst. The best system exhibited turnover frequencies up to 1.3 and 4.9 s–1 at overpotentials of 200 and 250 mV, respectively. This turnover frequency stands out among various molybdenum sulfide catalysts. The work demonstrates a novel strategy to control the assembly of hydrogen evolution reaction catalysts.