The synthesis of new nanohybrid catalysts with a tunable structure and the exploration of their synergistic behaviors have captured substantial attention. In this work, amorphous molybdenum disulfide/single‐walled carbon nanotubes (MoS2/SWNTs) composites are synthesized by a facile hydrothermal process with the assistance of l‐cysteine. We varied the mass ratio of sodium molybdate (the in situ Mo source) to SWNTs, this method provides a well‐defined pathway to enable the morphological control over the evolution of MoS2 from nanospheres to nanofilaments, nanorods, and nanosheets. Among the as‐obtained samples, the MoS2/SWNTs (1:1) hybrids, which displayed a 3 D architecture that consisted of nanorods, exhibited the highest activity in the hydrogen evolution reaction (HER). Compared with pure MoS2, the MoS2 nanosheets that decorate the SWNTs have more highly exposed active edges, and the SWNTs in the center of the MoS2/SWNTs nanorods can enhance the conductivity. We regulated the ratio between MoS2 and SWNTs to obtain a balance between the number of active sites and the conductivity of MoS2/SWNTs. Here, MoS2/SWNTs nanorods exhibited a low overpotential of 195 mV at 20 mA cm−2 and a low Tafel slope of 41 mV dec−1 for MoS2‐based HER catalysts.