Carbon nanotubes have attracted widespread attention as ideal materials for Lithium-ion batteries (LIBs) due to their excellent conductivity, mechanical flexibility, chemical stability and extremely large surface area. Here, three-dimensional (3D) silicon/carbon nanotube capsule composites (Si/CNCs) are firstly prepared via water-in-oil (W/O) emulsion technique with more than 75 wt% loading amount of silicon. CNCs with unique hollow sphere structure act as a 3D interconnected conductive network skeleton, and the cross-linked carbon nanotubes (CNTs) of CNCs can effectively enhance the strength, flexibility and conductivity of the electrode. This Si/CNCs can not only alleviate the volume expansion, but also effectively improve the electrochemical performance of the LIBs. Such Si/CNCs electrode with the unique structure achieves a high initial discharge specific capacity of 2950 mAh g−1 and retains 1226 mAh g−1 after 100 cycles at 0.5 A g−1, as well as outstanding rate performance of 547 mAh g−1 at 10 A g−1.