Rutile TiO2 nanorods are used for hybrid solar cells, photocatalysis, gas sensing, and energy storage devices. Here, we report in detail on the hydrothermal growth mechanism of these nanorods. A typical feature of TiO2 nanorods is a fine structure consisting of a multitude of small fingers. Thus, these nanocrystals are rather mesocrystalline than single crystalline, which has a great impact on chemical, electronic, and optoelectronic properties. This feature is also found in some other nanocrystalline materials, which are relevant for technical applications. Consequently, the understanding and control of this fine structure is an essential key to tune and improve device performances. In this study, we introduce a material-independent thermodynamic model, which is able to describe the formation of such fine structures. The model is based on two competing thermodynamic processes, namely crystallization and surface energy minimization, which are essential for the growth of crystals. Thereby, a non-equilibrium state between the two processes triggers the bundling of thin nanocrystals and leads to the formation of mesocrystalline nanorods. Based on the model the dimensions of the fine structure can be controlled using different growth temperatures, HCl concentrations, and post annealing in accordance to experimental observations.