The ion exchange processes and phase formation were studied by varying the properties of 1D barium titanate nanostructures. Temperature-, time- and alkalinity-dependent experiments were performed to study the BaTiO3 formation mechanism involving the generation of chemical sites which induced in situ transformation and dissolution-precipitation reactions occurring in a hydrothermal treatment procedure. As a result of the hydrothermal synthesis, BaTiO3 nano- and microrods with surface nanomaces and nanoparticle aggregates were formed in the temperature range of 160–210 °C, alkalinity range of 0.025–0.15 M and time range of 45–90 min. X-ray diffraction analysis revealed a significant increase in BaTiO3 material purity with increasing alkalinity from 0.025 to 0.15 M, even after a synthesis time of 45 min. In turn, Raman spectroscopy results showed that an increase in the synthesis time allowed not only BaTiO3 purity improvement, but also its phase composition control. The tetragonal phase of BaTiO3 was clearly observed after 6 h of hydrothermal synthesis at 210 °C and various alkalinities (from 0.025 to 0.15 M), while 45 and 90 min resulted in a mixture of cubic or tetragonal phases. Transmission electron microscopy demonstrated that BaTiO3 nanoparticles consisted of mainly tetragonal phases or a mixture of cubic and tetragonal phases, while BaTiO3 nano-/microrods preferably had cubic phases. Thus, variation of the temperature, time and alkalinity upon hydrothermal synthesis allowed the formation of BaTiO3 nano- and microstructures with different morphologies and phase compositions for diverse applications from biomedicine to microelectronics.