Metal oxide-based materials are attractive anode candidates for lithium-ion batteries (LIBs) because of their high theoretical capacity. However, these materials suffer from large volume expansion and poor stability of solid electrolyte interphase (SEI) during the charge-discharge process, casusing rapid capacity degradation. Herein, we report that Li3PO4-rooted and intact SEI in situ formed on the phosphate-modified SnO2/CNFs during cycling. The phosphate anions in the anode, could serve as the root to form Li3PO4 by bonding with Li ions and participate in the formation of the SEI, thus firmly anchoring and stabilizing the SEI layer. The rooted Li3PO4 and enriched LiF in the SEI could synergistically enhance the Li-ion diffusion, significantly reduce the volume expansion, and lead to ultrastable cycling performance over 1100 charge-discharge cycles at 1 A g-1. This work provides a new avenue for forming stable SEI rooted into the anode and inspires the development of interface engineering toward electrochemical energy storage.