Electrochemical performance of MoS2/graphene materials in Li-ion batteries is strongly dependent on the structure of individual components and their coupling in the hybrid. We present a comparative study of the materials produced by annealing of amorphous MoS3 deposited on the surface of multilayer graphene flakes at 500 °C, 800 °C, and 1000 °C in vacuum. X-ray photoelectron spectroscopy confirmed a transformation of MoS3 to MoS2 at these conditions. High-resolution transmission electron microscopy and Raman scattering showed a growth of in-plane size of MoS2 nanocrystals with a raise of annealing temperature. Electrochemical tests detected a gradual decrease of the specific capacity of the MoS2/graphene materials prepared at 500 and 800 °C and a stable performance for the material synthesized at 1000 °C even at high current densities. Based on the initial discharge-charge profiles, we associate this effect with in-plane size of MoS2 nanocrystals, which should decompose more easily when the size is small, due to the interaction of lithium with edge sulfur atoms.