Using Si as anode materials for Li-ion batteries remain challenging due to its morphological evolution and SEI modification upon cycling. The present work aims at developing a composite consisting of carbon-coated Si nanoparticles (Si@C NPs) intimately embedded in a three-dimensional (3D) graphene hydrogel (GHG) architecture to stabilize Si inside LiB electrodes. Instead of simply mixing both components, the novelty of the synthesis procedure lies in the in situ hydrothermal process, which was shown to successfully yield graphene oxide reduction, 3D graphene assembly production, and homogeneous distribution of Si@C NPs in the GHG matrix. Electrochemical characterizations in half-cells, on electrodes not containing additional conductive additive, revealed the importance of the protective C shell to achieve high specific capacity (up to 2200 mAh.g−1), along with good stability (200 cycles with an average Ceff > 99%). These performances are far superior to that of electrodes made with non-C-coated Si NPs or prepared by mixing both components. These observations highlight the synergetic effects of C shell on Si NPs, and of the single-step in situ preparation that enables the yield of a Si@C-GHG hybrid composite with physicochemical, structural, and morphological properties promoting sample conductivity and Li-ion diffusion pathways.