Two-dimensional layered structures have recently drawn worldwide attention because of their intriguing catalytic properties. Herein, we report 1T'-phase ammonium (A)- and methylammonium (MA)-intercalated MoS2 layered structures, synthesized by a one-step hydrothermal reaction. The MA-intercalated MoS2 exhibits excellent stability, as well as higher catalytic activity toward the hydrogen evolution reaction than the A-intercalated MoS2. First-principles calculations were used to assess the relative stabilities of the 2H and 1T' phases, showing a trend of 2H -> 1T' phase conversion with increasing concentrations of A or MA. The calculations consistently predicted a higher stability of the MA-intercalated complex, due to reduced repulsion between the positively charged MA moieties, which underlies the excellent catalytic performance.