Thermoplastic polyurethanes (TPU) usually exhibit multiple melting peaks in the differential scanning calorimetry (DSC) melting curves. It is of great significance to explore the origin of multiple melting peaks for fully understanding the phase transition behavior of TPU. In this paper, the cooling crystallization, isothermal crystallization and melting behavior of TPU are studied through DSC. It is found that four melting peaks show in the DSC melting curves of TPU under the fast cooling rate or low isothermal crystallization temperature and two melting peaks show up under the slow cooling rate or high isothermal crystallization temperature. By analyzing the crystallization kinetics and thermodynamic stability of TPU crystal, it is found that two crystalline forms—Form-II and Form-I are formed under different crystallization conditions. In addition, different crystalline forms exhibit different frequency of melt-recrystallization-melting during the heating, resulting in different multiple melting peaks behaviors.