The healing behavior of polyurethane (PU) elastomer is studied based on microcrack models by molecular dynamics simulation. It is found that PU elastomer has a self-healing capacity at 25, 50, and 70 °C when the molar ratio of polypropylene carbonate polyol (PPC), hexamethylene diisocyanate (HDI), and 1,6-hexamethylenediamine is 1:2:1. While the molar ratio of PPC, HDI, and 1,6-hexamethylenediamine is 1:1.33:0.33 or 2:3:1, the PU is never healed at 25, 50, and 70 °C. With the temperature rising, the self-healing rate is the fastest when the temperature is at 70 °C. Besides, the self-healing mechanism of PU elastomer is analyzed. It is found that the hydrogen bonds of Type 6 which are produced by urea groups and ester groups, Type 1 which are produced by urea groups and urea groups, and Type 2 which are produced by urea groups and urethane groups have made a great effect on self-healing behavior. Dynamic exchange is visually observed between different hydrogen bonds. Meanwhile, the strength, type, number of different types, and existence time of hydrogen bonds are elaborated. This study deepens the understanding of the mechanism about healing based on hydrogen bonding interactions.