The practical application of Si film anode is hindered severely, due to the very low active material loading. In current study, 3-dimensional nanostructured multilayer Si/Al film (3D-MSAF) of 1 μm in total Si thickness was prepared through chemical etching, electrochemical reduction and magnetron sputtering method and served as anode material of lithium-ion battery. This 3D-MSAF anode exhibits excellent cycle performance evidenced by a capacity as high as 1015 mAh g−1 after 120 charge–discharge cycles at the current density of 4.2 A g−1. Even at a much higher current density of 10.0 A g−1, the 3D-MSAF anode can still provide a capacity of 919 mAh g−1. However, the planar multilayer Si/Al film (P-MSAF) with the same Si thickness delivers only a capacity of 336 mAh g−1 after 55 cycles at 4.2 A g−1. The enhanced electrochemical performance is mainly attributed to the unique structure of the 3D-MSAF electrode, which could effectively accommodate the volume variation and improve the electronic conductivity.