Unique ordered TiO2 superstructures with tunable morphology and crystalline phase were successfully prepared by the use of different counterions. Dumbbell-shaped rutile TiO2 and nanorod-like rutile mesocrystals constructed from ultrathin nanowires, and quasi-octahedral anatase TiO2 mesocrystals built from tiny nanoparticle subunits were achieved. Interestingly, the obtained anatase mesocrystals have a fine microporous structure and a large surface area. The influence of the counterions in the reaction system is discussed and possible mechanisms responsible for the formation of the unique ordered TiO2 superstructures with different morphologies and crystalline phases are also proposed based on a series of experimental results. The obtained TiO2 superstructures were used as anode materials in lithium ion batteries, and exhibited higher capacity and improved rate performance; this is attributed to the intrinsic characteristics of the mesoscopic TiO2 superstructures, which have a single-crystal-like and porous nature.