A facile and reliable method has been developed to synthesize nanohybrids of anatase TiO2 nanoparticles-decorating carbon nanotubes (CNTs@TiO2). The nanohybrid displays a unique feature of having CNTs encapsulated inside and anatase TiO2 nanoparticles coating on the CNT surface. Comprehensive characterizations suggest that CNTs@TiO2 nanohybrids exhibit unique properties of CNTs and TiO2 nanoparticles with one-dimensional structure, excellent electrical conductivity, high surface area, and good biocompatibility. The electrochemical properties of CNTs@TiO2 nanohybrids were systematically investigated, it was revealed that the CNTs@TiO2 nanohybrids showed great promise as anode materials of microbial fuel cells (MFCs). Compared with pure TiO2 nanoparticles and CNTs alone, CNTs@TiO2 nanohybrids exhibited a much higher output current, power density, and Coulombic efficiency when used as anode materials of MFCs. The as-developed synthetic route opens up a new avenue for designing CNTs-based nanohybrid materials for various applications benefiting from the synergetic effect among constituents.