We report the synthesis of a novel branched nano-heterostructure composed of SnO2 nanowire stem and alpha-Fe2O3 nanorod branches by combining a vapour transport deposition and a facile hydrothermal method. The epitaxial relationship between the branch and stem is investigated by high resolution transmission electron microscopy (HRTEM). The SnO2 nanowire is determined to grow along the [101] direction, enclosed by four side surfaces. The results indicate that distinct crystallographic planes of SnO2 stem can induce different preferential growth directions of secondary nanorod branches, leading to six-fold symmetry rather than four-fold symmetry. Moreover, as a proof-of-concept demonstration of the function, such alpha-Fe2O3/SnO2 composite material is used as a lithium-ion batteries (LIBs) anode material. Low initial irreversible loss and high reversible capacity are demonstrated, in comparison to both single components. The synergetic effect exerted by SnO2 and alpha-Fe2O3 as well as the unique branched structure are probably responsible for the enhanced performance.