The NVH (Noise, Vibration, and Harshness) characteristics of micro-motors used in vehicles directly affect the comfort of drivers and passengers. However, various factors influence the motor’s structural parameters, leading to uncertainties in its NVH performance. To improve the motor’s NVH characteristics, we propose a method for optimizing the structural parameters of automotive micro-motors under uncertain conditions. This method uses the motor’s maximum magnetic flux as a constraint and aims to reduce vibration at the commutation frequency. Firstly, we introduce the Pareto ellipsoid parameter method, which converts the uncertainty problem into a deterministic one, enabling the use of traditional optimization methods. To increase efficiency and reduce computational cost, we employed a data-driven method that uses the one-dimensional Inception module as the foundational model, replacing both numerical models and physical experiments. Simultaneously, the module’s underlying architecture was improved, increasing the surrogate model’s accuracy. Additionally, we propose an improved NSGA-III (Non-dominated Sorting Genetic Algorithm III) method that utilizes adaptive reference point updating, dividing the optimization process into exploration and refinement phases based on population matching error. Comparative experiments with traditional models demonstrate that this method enhances the overall quality of the solution set, effectively addresses parameter uncertainties in practical engineering scenarios, and significantly improves the vibration characteristics of the motor.