Wulff-shaped and nanorod-like nanoporous mesocrystals constructed from ultrathin rutile TiO2 nanowires were successfully fabricated for the first time in the presence of the surfactant sodium dodecyl benzene sulfonate (SDBS). SDBS played a key role in the homoepitaxial self-assembly process, in which titanate nanowires were used as the primary building blocks for forming mesocrystals accompanying with a simultaneous phase transition. The nanoporous rutile TiO2 mesocrystals have a large surface area and were subjected to detailed structural characterization by means of X-ray diffraction (XRD), scanning and transmission electron microscopy (SEM/TEM) including high-resolution TEM (HRTEM) and selected area electron diffraction (SAED). Furthermore, the nanoporous rutile TiO2 mesocrystals were applied as the electrode materials in rechargeable lithium-ion batteries and demonstrated a large reversible charge–discharge capacity, excellent cycling stability and high rate performance. These properties were attributed to the intrinsic characteristic of the mesoscopic structured TiO2 with nanoporous nature and larger surface area (which favored fast Li-ion transport), as well as the presence of sufficient void space to accommodate the volume change.