We demonstrate the synthesis of order-aligned Mn3O4 nanostructures by electrochemically depositing Mn3O4 on a pre-fabricated Cu nanowire array current collector. When used as an electrode for lithium-ion batteries, it exhibits a capacity up to 637 and 494 mA h g−1 after 100 cycles at a current rate of 10 C and 20 C (10 C = 9.4 A g−1), respectively. The excellent cycling performance and superior rate capability can be attributed to the good electrical contact, fast electron transport and good strain accommodation of the order-aligned nanostructured electrodes. The relationship between the thickness of the Mn3O4 film and its electrochemical performance has also been investigated.