One of the important objectives for the development of enhanced lithium-ion batteries is developing high-performance silicon-based anodes with durable operational capability. Herein, a three-dimensional graphene-decorated core-shell Si/C composite is fabricated by the in-situ polymerization of organic pyrrole molecule and pyrolysis process, in which the melamine formaldehyde resin is subtly used as three-dimensional porous framework to offer abundant loading area for the uniform dispersion of active silicon nanoparticles. Meanwhile, the core-shell structure deriving from polypyrrole in the composite can effectively buffer the volume change of silicon ingredient and avoid the direct contact with the electrolyte during the cycling process, leading to the improved structural stability and electrochemical performance. The outermost layer of graphene nanosheets is designed to enhance the electrical conductivity of the electrode. As a result, the synthesized Si/C/graphene composite exhibits a high capacity and excellent cycling performance. This work reveals that combining a three-dimensional carbon substrate with a core-shell structure might be a promising solution for anode materials with obvious volume transformation.