Silicon has been recognized as the most promising anode material for high-capacity lithium ion batteries. However, its large volume variation during the charge-discharge process results in electrode pulverization and fast capacity loss on cycling. The paper reports a facile synthesis of phenylalanine-functionalized graphene quantum dots (PF-GQD) through the pyrolysis of citric acid and phenylalanine. The PF-GQD was coated on the surface of silicon nanoparticles (SiNP) and then treated by thermal annealing in Ar/H2 to obtain PF-GQD@SiNP composite. The PF-GQD coating layer not only improves the electrical conductivity, but also effectively prevents the direct contact of silicon surface with the electrolyte molecules. The composite electrode exhibits an excellent electrochemical performance for lithium ion batteries. The specific capacity is 4066mAhg−1 at 50mAg−1, 3796mAhg−1 at 100mAg−1 and 1820mAhg−1 at 1000mAg−1. The capacity can remain 3068mAhg−1 after 100 cycles at 100mAg−1. As a control sample, alanine-functionalized graphene quantum dots (AF-GQD) was also prepared and used for the fabrication of AF-GQD@SiNP composite. The result shows that the electrochemical performance of PF-GQD@SiNP is much better than that of AF-GQD@SiNP. The improvement is attributed to the benzene ring at the edge of graphene sheets. Its introduction creates a wider and finer energy level of electron and well-defined steric structure compared to AF-GQD, which further accelerates the electron transfer and electrolyte transport and leads to an improved electrochemical performance. In addition, the study also provides an economic, eco-friendly and facile method for the fabrication of silicon-based anode materials for next generation high-performance lithium ion batteries.