A three-dimensional (3D) carbonaceous aerogel derived from biomass bacterial cellulose (BC) is introduced as a flexible framework for iron oxides in Li-ion batteries (LIBs). The 3D carbonized BC (CBC) with highly interconnected nanofibrous structure exhibits good electrical conductivity and mechanical stability. The amorphous Fe2O3 is tightly coated on the nanofibers of CBC through a simple in situ thermal decomposition method. The obtained amorphous Fe2O3 anode (denoted as A-Fe2O3@CBC) exhibits stable cycling performance and high rate capability when assembled into a half-cell, which is supposed to benefit from the well-dispersed Fe2O3 nanoshells and the hierarchical pores in A-Fe2O3@CBC composite. The rational design of the nanostructure could improve the transportation of electrons/ions and effectively alleviate volume changes of Fe2O3 during the electrochemical cycling. Meanwhile, the amorphous nature of the Fe2O3 in anode provides an enhanced capacitive-like lithium storage and flexible structure of the active materials, resulting in much higher specific capacity and longer cycle life when compared with its crystalline counterpart. This work provides a promising approach to design and construct the flexible metal oxide anode materials based on 3D carbonaceous aerogel for high-performance LIBs.