MoO2 with low electrical resistivity and high specific capacity as anode for lithium ion batteries is hindered because of its large volume variation during Li+ insertion/extraction process, which leads to fast capacity fading. Herein, three-dimensional (3D) core-shell MoO2@few-layered MoS2 covered by S-doped graphene (MO/MS/SG) aerogel has been fabricated through hydrothermal reaction and freeze-drying process together with sulfidation. MoO2 nanoparticles coated by few-layer MoS2 can promote good dispersion of MoO2 nanoparticles and avoid the restacking of MoS2. S doping in graphene can increase the defects and active sites. S-doped graphene aerogel as flexible framework and conductive network not only provides the transmission path for ions and electrons, but also maintains the structural integrity of electrode during cycles. Core-shell MoO2@few-layer MoS2 hybrid well-dispersed in S-doped graphene matrix buffers the volume changes during cycles and contributes to high reversible capacity. Free-standing electrode without binder and current collector prevents the separation of electrode materials from current collector during cycles. Benefitting from the unique structures, the MO/MS/SG aerogel as anode for lithium ion battery exhibits high reversible capacities of 683 mAh g−1 at 0.1 A g−1 after 100 cycles and 533 mAh g−1 at 0.5 A g−1 after 350 cycles together with excellent rate capability. This work demonstrates the potential application of the Mo-based materials in lithium ion batteries.