Developing robust micron porous silicon (MPSi) anodes has received much attention for next-generation lithium (Li)-ion batteries. Nevertheless, localized high stresses during fabrication and cycling tremendously bring about structural failure and capability degradation. Herein, a flexible-rigid covalent nano-template comprising a buffer skin and packing shell fabricated via an in situ assembly was designed to synergistically regulate the MPSi anode structure organization. Such a unique structure could significantly tune the internal/interface interactions and accommodate the volume change, resulting in an outstanding structure stability and excellent performance. In particular, this anode delivered a high capacity of 1014 mA h g⁻¹ at 1000 mA g⁻¹ after 800 cycles and 960 mA h g⁻¹ at 2000 mA g⁻¹ after 400 cycles at a high area loading of 2.9 mg cm⁻². Moreover, the full cell including this MPSi anode and the commercial LiFePO₄ cathode exhibited a 95% high capacity retention after ∼200 cycles. Our work offers insights into the novel surface regulation of a promising MPSi anode for high-performance and ultra-robust Li-ion batteries.