This paper introduces a large-scale and facile method for synthesizing low crystalline MoO3/carbon composite microspheres, in which MoO3 nanocrystals are distributed homogeneously in the amorphous carbon matrix, directly by a one-step spray pyrolysis. The MoO3/carbon composite microspheres with mean diameters of 0.7 µm were directly formed from one droplet by a series of drying, decomposition, and crystalizing inside the hot-wall reactor within six seconds. The MoO3/carbon composite microspheres had high specific discharge capacities of 811 mA h g−1 after 100 cycles, even at a high current density of 1.0 A g−1 when applied as anode materials for lithium-ion batteries. The MoO3/carbon composite microspheres had final discharge capacities of 999, 875, 716, and 467 mA h g−1 at current densities of 0.5, 1.5, 3.0, and 5.0 A g−1, respectively. MoO3/carbon composite microspheres provide better Li-ion storage than do bare MoO3 powders because of their high structural stability and electrical conductivity.