Hydrogen bonding has been reported to be crucial to crystallization behavior and phase structure and consequently the properties of polyurethane (PU). However, the relationship between hydrogen bonds, crystallization, and phase structure still remains a hot topic of researches because it determines the final performance of materials. Herein, a 5‐(2‐hydroxyethyl)‐6‐methyl‐2‐aminouracil (UPy) group capable of forming multiple hydrogen bonds is incorporated into polyurethanes (PUUPys) to ascertain the effect of hydrogen bonds on the structure and properties of PU. It is found that the content of hydrogen bonds increases with UPy amount, which induces obvious changes in crystallization behavior of soft and hard segments. The varied crystallization further promotes microphase separation, and makes phase structure transform from two‐phase (crystalline soft domains and amorphous domains) with lower UPy amount into three‐phase (crystalline soft domains, crystalline hard domains, and amorphous domains) with higher UPy content. The adjustable hydrogen bonding and phase structure endow PUUPy with tunable mechanical properties, which, in combination with the inherent self‐healing characteristics of UPy groups, indicate great potentials of PUUPys in smart materials. This work demonstrates the principle of changing hydrogen bonding to obtain best performance in structural design of polyurethanes.