We demonstrate the synthesis of SiGe-based three-dimensional (3D) porous nanostructures via a template-assisted method. When tested as electrode in lithium-ion batteries, it exhibits a reversible capacity as high as 1311 mAh g−1 after 45 cycles at a current density of 4 A g−1. Even at a super high current rate of 16 A g−1, the electrode can deliver a stable capacity of about 1047 mAh g−1. The great cycling performance and superior rate capability can be attributed to the good electrical contact, fast electron transport and good strain accommodation of the 3D nanostructure of the porous electrode.