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Polyurea (PUR) has been widely used as a protective coating in recent years. In order to complete the understanding of the relationship between PUR microstructure and its energy absorption capabilities, the mechanical and dynamic performance of PURs containing various macrodiol structural units were compared using material characterization techniques and molecular dynamic simulation. The results showed that the PUR polycarbonate diols formed as energy absorbing materials showed high tensile strength, high toughness, and excellent loss factor distribution based on the comparison of stress–strain tensile curves, glass transition temperatures, phase images, and dynamic storage loss modulus. External energy from simple shear deformation was absorbed to convert non-bond energy, in particular, based on fractional free volume, interaction energy, and total energy and hydrogen bond number change from the molecular dynamic simulation. Hydrogen bonds formed between soft segments and hard segments in the PURs have been proven to play a significant role in determining their mechanical and dynamic performance. The mechanical and dynamic properties of PURs characterized and tested using experimental techniques were quantified effectively using molecular dynamic simulation. This is believed to be an innovative theoretical guidance for the structural design of PURs at the molecular level for the optimization of energy absorption capabilities. [ABSTRACT FROM AUTHOR]