Silicon (Si) is a promising high-capacity anode material for the next-generation of rechargeable lithium ion batteries (LIBs). Though there are formidable challenges from the large volumetric change during lithiation, well-designed nanostructure and reduced size of Si can remarkably alleviate the negative effects. Herein we apply a magnesiothermic reduction process to synthesize interconnected Si nanoparticles in large quantities. Earth abundant clay of halloysite with tubular structure has been used as silica precursor after acid washing. A high Si yield can be achieved upon pressing the precursor powder into a pallet before reduction. The obtained interconnected Si nanoparticles exhibit a high specific capacity of 3752.4 mA h g−1 for the first cycle at1 A g−1 and 1469.0 mA h g−1 after 400th cycles at current density of 3.5 A g−1. Even tested at 5 A g−1 for 1000 cycles, a high capacity of 735.1 mA h g−1 is obtained. The rate capability is also evaluated and a high capacity of 1050 mA h g−1 is achieved at 10 A g−1.