Pompon-like MnO/carbon nanotube (CNT) composite microspheres have been prepared by the pyrolysis of Mn3O4 and CNT mixtures. These microspheres are constructed by combining MnO nanocrystallines with CNT scaffolds to form the interconnected MnO-modified CNT networks. The three-dimensional composite structures are superior to the simple mixture of MnO and CNT in combination with each advantage, such as the inhibited aggregation, large porosity, high conductivity and enhanced mechanical strength. The lithium ion batteries based on MnO/CNT composite microspheres as anodes exhibit a high specific capacity of 841mAhg−1 after 200 cycles at 0.1Ag−1. Even at 0.38Ag−1, the capacity could be still kept at 741mAhg−1 after 250 cycles. The significant results might be attributed to the unique space grid structure and specific composition, including the CNT crossing-linked MnO for high dispersion of nanoparticles, abundant porous channels for electrolyte diffusion, excellent electronic conductivity for electron transport and durable structure for repeated electrochemical reactions.