The transition metal dichalcogenides have instigated a lot of interest as harmonic generators due to their exceptional nonlinear optical properties. Here, the molybdenum disulfide (MoS2) molecular structures with dopants being in a plasma state are used to demonstrate the generation of intense high-order harmonics. The MoS2 nanoflakes and nickel-doped MoS2 nanoflakes produced stronger harmonics with higher cut-offs compared with Mo bulk and MoS2 bulk. Conversely, the MoS2 with nickel nanoparticles and carbon nanotubes (MoS2-NiCNT) produced weaker coherent XUV emissions than other materials, which is attributed to the influence of phase mismatch. The influence of heating and driving pulse intensities on the harmonic yield and cut-off energies are investigated in MoS2 molecular structures. The enhanced coherent extreme ultraviolet emission at ~32 nm (38 eV) due to the 4p-4d resonant transitions is obtained from all aforementioned molecular structures, except for MoS2-NiCNT.