Anatase TiO2 (a-TiO2) mesocrystal has been regarded as a superior photocatalyst because of its high crystallinity and large surface area. In this work, a-TiO2 mesocrystals were hydrothermally synthesized under various process temperatures and their crystallinity, morphology, and photocatalytic performance were evaluated. An elliptical a-TiO2 mesocrystal with truncated bipyramidal subunits was formed when the hydrothermal temperature was over 120 °C. While the crystallinity of the sample was enhanced, the surface area decreased as the temperature was increased, which was due to the increased size and reduced number of subunits. While the photocatalytic activity improved at temperatures up to 180 °C, it slightly degraded at 210 °C, suggesting that the crystallinity, rather than the surface area, was a dominant factor. This phenomenon was probably due to the existence of by-products covering the subunit surface and interrupting the reaction between a-TiO2 and methylene blue. Our work suggests that, while a-TiO2 mesocrystal is an excellent photocatalyst, it is essential to eliminate residual by-products in order to increase actual photocatalytic active sites.