SnO2 with high theoretical capacity has long suffered from its instinct large volume variation and low electrical transport linked to poor cycling stability and rate performance. Here we present the heterogeneous branched core–shell SnO2–PANI nanorod arrays which have been successfully designed and fabricated by an efficient and facile hydrothermal treatment followed by electrodeposition. The heterogeneous core–shell SnO2–PANI nanorod arrays exhibit a high reversible capacity of 506mAh/g after 100 cycles, resulting the capacity fading of 0.579% per cycle between 20 and 100 cycles, much lower than that of nanosheet-assembled hierarchal SnO2–PANI nanorod arrays (1.150%) and bare SnO2 nanorod arrays (1.151%). At high current density of 3000mA/g, heterogeneous core–shell SnO2–PANI nanorod arrays maintain a capacity of 660mAh/g after the current density returns to 100mA/g, 3 times as high as that of nanosheet-assembled hierarchal SnO2–PANI nanorod arrays (206mAh/g) and 6 times as high as that of bare SnO2 nanorod (124mAh/g). The enhanced electrochemical performance can be attributed to the branched conductive PANI shells, which not only release the stress of volume expansion and maintain mechanical integrity during cycling, but also realize three dimensional transport for electrons. Our work demonstrates a great potential for the application of heterogeneous branched core–shell PANI–SnO2 nanorod arrays for lithium batteries.