Na2Ti6O13 nanowhiskers with controllable morphologies were prepared via a simple molten salt evaporation method using a small quantity of NaCl-KCl as molten salt. The synthesized products were characterized by X-ray diffraction, field emission scanning electron microscope, and transmission electron microscope. The optimal growth dynamic conditions for synthesis of Na2Ti6O13 nanowhiskers were also studied and discussed. According to thermogravimetry-differential scanning calorimetry analysis, the calcination process was designed to include two stages, lower temperature for reaction and higher temperature for evaporation of molten salt. Nanowhiskers and nanorods with different diameters can be obtained under different evaporation conditions. By comparing residual amounts of NaCl-KCl on product surfaces calculated by determined kinetic equation and experimental results only using NaCl as molten salt, it was revealed that the molten salt evaporation rates could play an important role on the morphologies of Na2Ti6O13. A formation mechanism was provided based on nucleation and growth model and an oriented aggregation process to understand different morphologies of Na2Ti6O13. This simple molten salt evaporation method would be suitable for large scale synthesis.