A flexible carbonized cotton covered by graphene/Co-doped SnO2 (CGN/SnO2-Co) composite is prepared by in situ and subsequent microwave method, then followed by thermal annealing treatment. The SnO2 nanoparticles with ultra-small size are uniform decorated on the CGN framework, and Co element has been successful doping into SnO2. It is found that doping process does not affect the phase structure of SnO2, but great influence the morphology, the electrical conductivity, and the electrochemical properties on the composites. As a free-standing and binder-free anode for lithium-ions batteries, the discharge capacity of CGN/SnO2-Co have a high value of 549.6mAhg−1 (1996μAcm−2) after 100 cycles at a current density of 100mAg−1, which is much higher than those of cotton covered by graphene/SnO2 (CGN/SnO2) and cotton covered by graphene/Co3O4 (CGN/Co3O4) at the same current. The improved performance of CGN/SnO2-Co can be attributed to the highly stable and conductive CGN framework, ultra-small size of SnO2 nanoparticles, and Co doping effect. It is reasonable to believe that this work has a great potential improve the performance of energy storage devices.