We demonstrate a novel strategy for the well-controlled preparation of MnO2 hierarchical nanostructures, i.e. MnO2 submicron fibers composed of nanosheets or nanorods with different crystalline phases (delta- and alpha-MnO2), by integrating electrospinning, hydrothermal synthesis and subsequent heat-treatment. Specifically, delta-MnO2 submicron fibers with different surface morphologies are synthesized via a template-assisted hydrothermal process and by using electrospun nanofibers (Polyacrylonitrile (PAN), oxidized PAN and carbonized PAN nanofibers); after that, alpha-MnO2 nanostructures composed of different nanorod-like nanostructures are prepared by the heat-treatment of the corresponding delta-MnO2 nanostructures at 700 degrees C in air. The effects of the reaction parameters (i.e. different templates and growth conditions) on the morphology and crystal phase are investigated in detail. The results demonstrate that the microstructures and structural conversion of the MnO2 nanostructures are closely correlated with the initial templates. Furthermore, the potential application of the alpha-MnO2 hierarchical nanostructures as the anode for a lithium ion battery is studied, and the results show that the pine-like alpha-MnO2 exhibits a stable capacity up to 380 mA h g(-1) after 150 cycles.