The utilization of silicon based anode materials for lithium-ion batteries is hindered by their low intrinsic electronic conductivity, unstable cycling behavior and complex scalable synthesis of nano silicon. Herein, we propose a step-by-step synthesis route to fabricate three-dimensional (3D) graphene nanosheets loaded with Si nanoparticles for lithium ion batteries. For this purpose, silica is deposited on the surface of graphene oxide firstly through a hydrolysis process. After that, a further in situ magnesiothermic reduction is carried out. In an attempt to fine-tune the mass ratio of graphene and Si, different amount of tetraethyl orthosilicate was applied during the hydrolysis process. The 3D graphene as supporting sheets could not only provide position for the firmly attached Si nanoparticles but also enhance the electronic conductivity and accommodate large volume changes of Si nanoparticles. As a result, the properly designed Si@G-2 exhibits an excellent electrochemical performance and rate capability, showing capacity retention of 90.9% after 100 cycles at 1Ag−1 and specific capacity around 500mAhg−1 at 20Ag−1. This synthetic route demonstrates an efficient method for the controlled synthesis of graphene nanosheets loaded with Si nanoparticles with excellent electrochemical performance, which may facilitate its commercial applications.