In this work, by adopting the united atom model of cis‐1,4‐poly(butadiene) (PB), we systemically investigate the effect of the chain structure on the glass transition temperature (Tg) and the viscoelastic property of PB system. First, we analyze the atom translational mobility, bond reorientation dynamics, torsional dynamics, conformational transition rate, and dynamic heterogeneity of the PB chains with different chain structures in detail by determining the corresponding Tg. In addition, our results clearly indicate that with the decrease of the amount of the free end atoms of PB via the end‐linking method, the mobility of the PB chains quickly decreases. As a result, the Tg of the PB chains gradually increases. Depending on the chain structure and the calculation method, the Tg of the PB chains varies from 154 to 240 K. In addition, the temperature dependence of the dynamic properties has different Arrhenius behaviors above and below Tg. The calculated activation energy varies from 7.37 to 16.37 KJ/mol for different chain structures above Tg, which can be compared with those for other polymers. In addition, through the end‐linking approach the strong interaction between the PB chains improves the storage modulus G′ and the loss modulus
G″. Meanwhile, the immobility of the free end atoms effectively reduces the friction loss of the chains under the shear field, which is reflected by the low loss factor
tanδ. In summary, this work can further help to understand the effect of the chain structure on the dynamic properties of the PB chains. Meanwhile, it provides an effective approach to reduce the energy loss during the dynamic periodic deformation, which can cut the fuel consumption via the end‐linking method. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017, 55, 1005–1016