The relevance of this research stems from the necessity to enhance existing vibration-compensation systems for reducing vibrational loads on power units of mainline pumping units (MPUs). Algorithms and computational results of the spatial vibration state of the vibration-compensation system (VCS) for MPUs under various operational regimes are presented. Mathematical and spatial finite-element models, as well as versatile digital prototypes of the VCS, have been developed. The novelty of the findings lies in the developed digital prototype of the MPU, which offers broad capabilities for accounting for design-technological factors, accommodates diverse operational regimes, and exhibits high precision and computational efficiency. The practical significance of the work is that the developed simulation methodology based on digital prototypes of the MPU VCS enables the analysis of vibrational impacts from electric motors, pumps, and load-bearing frames. Comprehensive computational studies of the stress-strain state of the VCS frame were performed, and the system’s natural frequencies during operation were evaluated. The objective of this work is to study the behavior of the pumping unit when replacing elastomeric supports in the compensation system with hydrofilm dampers. An indisputable advantage of the developed digital model is its foundation for a universal methodology to assess the effectiveness of vibration compensators in the MPU VCS. A unique digital prototype of the MPU was developed considering the engineered VCS. The feasibility of using a finite-element-based digital prototype for evaluating vibrational loading on MPUs is substantiated. Numerical experiments using the MPU’s digital twin established that implementing hydrofilm dampers in the VCS reduces peak dynamic stresses by 18%. Values of axial and resultant displacements of the MPU using hydrofilm and elastomeric dampers in the VCS were obtained, measuring 11.1 mm and 10.0 mm, respectively.