Cobalt oxides are attractive high-capacity anode materials in lithium ion batteries yet suffer from fast capacity fading and low rate capability. Herein, we have prepared well-dispersed cobalt oxide nanoparticles encapsulated within a flexible single-walled carbon nanotubes matrix (marked as Co3O4 NPs@SWCNT), for the first time, through a facile evaporation-induced self-assembly (EISA) of single-walled carbon nanotubides (SWCNTDs). By varying the loading amount of Co3O4 content in the composite, the optimal Co3O4 NPs@SWCNT exhibits a high capacity of 1286mAhg−1 after 140 cycles at 100mAg−1. When the specific current returns from 5000mAg−1 to 100mAg−1, it still maintains a specific capacity of 1109mAhg−1, demonstrating remarkable cycling stability and high rate capability. Moreover, the optimal Co3O4 NPs@SWCNT demonstrates superior prolonged cycling stability for over 200 and 600 cycles at extremely high specific currents of 1000 and 2000mAg−1, respectively. Such impressive electrochemical properties are mainly ascribed to the synergic effect of Co3O4 nanoparticles and SWCNTs in the heterostructure, in which the robust SWCNTs not only offer excellent strain accommodation of the encapsulated Co3O4 upon long-term cycling, but also significantly enhance overall electric conductivity and mechanical stability of the electrodes. The facile and effective strategy demonstrated here can be extended to design various SWCNT-based hybrid nanostructures for applications in supercapacitors, water splitting and other fields.