Phase-pure ZnMn2O4 nanopowders and their aggregated microsphere powders for use as anode material in lithium-ion batteries were obtained by a simple spray drying process using zinc and manganese salts as precursors, followed by citric acid post-annealing at different temperatures. X-ray diffraction (XRD) analysis indicated that phase-pure ZnMn2O4 powders were obtained even at a low post-annealing temperature of 400 °C. The post-annealed powders were transformed into nanopowders by simple milling process, using agate mortar. The mean particle sizes of the ZnMn2O4 powders post-treated at 600 and 800 °C were found to be 43 and 85 nm, respectively, as determined by TEM observation. To provide practical utilization, the nanopowders were transformed into aggregated microspheres consisting of ZnMn2O4 nanoparticles by a second spray drying process. Based on the systematic analysis, the optimum post-annealing temperature required to obtain ZnMn2O4 nanopowders with high capacity and good cycle performance was found to be 800 °C. Moreover, aggregated ZnMn2O4 microsphere showed improved cycle stability. The discharge capacities of the aggregated microsphere consisting of ZnMn2O4 nanoparticles post-treated at 800 °C were 1235, 821, and 687 mA h g−1 for the 1st, 2nd, and 100th cycles at a high current density of 2.0 A g−1, respectively. The capacity retention measured after the second cycle was 84%.