From a molecular perspective, the viscosity of bitumen is determined by the motions of its molecules. Therefore, it is crucial to establish a relationship between different fractions of bitumen and their corresponding viscosities. In order to achieve this objective, the utilization of molecular dynamics simulation methodology proves to be promising. However, current practices indicate that there is no consensus on a specific simulation framework that can accurately simulate bitumen with predetermined fractions. Hence, this study proposes an improved averaging strategy as a modification to the existing simulation method. Specifically, the analysis focused on examining the rigidity and flexibility of pyrrole in bitumen to establish a foundation for vector selection. Furthermore, the influence of sampling time and interval was thoroughly discussed. To predict bitumen viscosity using the Debye-Stokes-Einstein (DSE) method, the modified Kohlrausch-Williams-Watts (mKWW) function was employed to fit self-autocorrelation functions. The findings revealed that neglecting the relative flexibility of branch chains would be inadequate when describing self-autocorrelation functions. Additionally, it is crucial to consider both sampling time and interval in order to obtain a more realistic representation of self-autocorrelation functions. This study demonstrates the feasibility of an improved averaging strategy for enhancing viscosity calculation accuracy.