Accurate and quantitative identification of unbalanced force during operation is of utmost importance to reduce the impact of unbalanced force on a hypergravity centrifuge, guarantee the safe operation of a unit, and improve the accuracy of a hypergravity model test. Therefore, this paper proposes a deep learning-based unbalanced force identification model, then establishes a feature fusion framework incorporating the Residual Network (ResNet) with meaningful handcrafted features in this model, followed by loss function optimization for the imbalanced dataset. Finally, after an artificially added, unbalanced mass was used to build a shaft oscillation dataset based on the ZJU-400 hypergravity centrifuge, we used this dataset to train the unbalanced force identification model. The analysis showed that the proposed identification model performed considerably better than other benchmark models based on accuracy and stability, reducing the mean absolute error (MAE) by 15% to 51% and the root mean square error (RMSE) by 22% to 55% in the test dataset. Simultaneously, the proposed method showed high accuracy and strong stability in continuous identification during the speed-up process, surpassing the current traditional method by 75% in the MAE and by 85% in the median error, which provided guidance for counterweight and guaranteed the unit’s stability.