The interface between MoS2 and carbon components plays an important role in the performance of the hybrid material in Li-ion batteries. To enhance the interfacial interactions, holey graphene (HG) layers are used as a support for the forming MoS2, and the compression of components is used during the synthesis. Initial compositions, obtained by deposition of MoS3 on the surface of HG stacks, are annealed at 400–600 °C and 100 bar. Using a set of characterization methods, the synthesis products are studied and it is found that the hole boundaries anchor MoS2 via covalent C–Mo coupling, while the applied pressure assists in the development of a thin MoS2 coating. The number of layers and their lateral dimensions are dependent on the synthesis temperature. The tests of Li-ion half-cells detected higher values of specific capacity for MoS2/HG hybrids synthesized under compression. Enhanced interaction between the components prevents the destruction of MoS2 during discharging–charging of electrodes, and the capacity increases due to the accommodation of lithium between the layers of MoS2 and HG. The structural features of MoS2/HG hybrids stipulate growth of specific capacity with long-term cycling to ≈1200 mA h g−1 at a current density of 0.5 A g−1.