In this study, polyurethane (PU) hydrogels were synthesized via mercapto curing reaction to elucidate the effect of molecular interactions between isocyanate and soft segments on the properties of hydrogels. Further, the mesh size, mechanical properties, hydrophilicity, and biological properties of the PU hydrogels were determined. In the isocyanate series, the structural regularity and rigidity of 4,4′‐dicyclohexylmethane diisocyanate (HMDI) favored the formation of hydrogel materials with small mesh size, high modulus, and low water absorption. In contrast, l‐lysine diisocyanate (LDI) favored the materials with large mesh size, low modulus, and good hydrophilicity. In the soft‐segment series, the strong hydrogen bonds of polycarbonate diol (PCDL) favored the formation of materials with small mesh size, dense cross‐link points, and high modulus, whereas weak hydrogen bonds of polytetrahydrofuran ether glycol (PTMG) favored the hydrogel materials with small mesh size, few crosslink points, and low modulus. PU hydrogels exhibit excellent cytocompatibility, anti‐cell adhesion, and anti‐inflammatory properties. Therefore, this study offers valuable insights into understanding the chain structure and macroscopic properties, thus contributing to preparing PU hydrogels with varying performances, as desired.