The degree of crosslinking and distribution of crosslinking points have a significant impact on the mechanical properties of rubber. The molecular dynamics models of polyisoprene rubber (IR) with different crosslinking degrees and crosslinking distributions were constructed, and uniaxial tensile and tensile recovery simulations were carried out. By analyzing the dynamic characteristic parameters and tensile deformation of molecular chains, the micro mechanism of the influence of crosslinking degree and crosslinking distribution on the dynamic and static mechanical properties of polyisoprene rubber (IR) was explored. The results show that the higher the crosslinking degree and the more uniform of crosslinking distribution during stretching process are, the greater the stiffness of material is, and the smaller the contribution of viscosity to stress is. Analysis has found that during tensile deformation, the degree of deformation and uneven distribution of molecular chains increases, and the relative slip of molecular chains increases, leading to an increase in the viscosity characteristics of material. By increasing the degree of crosslinking and uniformity of crosslinking distribution, the constraint effect on molecular chains can be increased, and the non-uniformity of molecular chain deformation can be reduced, thereby reducing the viscosity characteristics of material. The results of this study provide a reference for revealing the deformation mechanism of this type of material, improving its mechanical properties, and better application.