Three-dimensional (3D) nanostructure is the key to the miniaturization of nonlinear photonic and electronic devices. Because of the great demand on the ultra-small nanostructures, the novel nanofabrication technologies with flexible 3D silicon (Si) fabrication capability are of great importance. Herein, by combining Ga+ FIB implantation and ICP dry etching processes, we proposed a novel Ga+ FIB implantation assisted maskless dry etching technology for direct fabrication of 3D Si nanostructures. We found that the implanted Ga+ induced amorphization layer in Si substrate acts as the ‘quasi-mask’ during the ICP dry etching process. The increase of Ga+ concentration in amorphization layer of Si substrate improves the etching resistance of the area. Moreover, enabled by high resolution and flexibility of FIB, the proposed technology is capable of directly fabricating various 3D Si nanostructures in a simple way, such as 3D nanoscale artificial bowtie arrays with sub-10 nm gaps, multi-scale 3D Si nanostructures with arbitrary patterns. More importantly, the proposed technology is compatible to current semiconductor manufacturing process. Benefiting by the advantages of simplicity and high efficiency, the proposed maskless dry etching process promises great application potential in the fields of nonlinear photonics and micro-electronics.