Despite achieving considerable success, the fault diagnosis methods will still be disturbed by noisy labels, this causes the model’s degradation and reduced diagnostic precision. Focused on solving the above issues, a robust intelligent fault diagnosis approach for rotating machinery under noisy labels is proposed. Firstly, we maintain two deep neural networks (DNNs) and alternatively execute parameters updating and models optimization by referring to the Co-teaching strategy, which can maximize filtering different error types and implement pre-training of DNNs. Secondly, adopting a two-component Gaussian mixture model (GMM) to fit training dataset’s cross-entropy (CE) loss and realize the clean and noisy labels division according to the threshold. Then, a data augmentation method called Mixup operation is employed in semi-supervised learning (SSL) to increase noise robustness and avoid error accumulation, subsequently, performing fine-tuning and correction for clean and noisy samples. Challenging experiments on a transmission gearbox dataset under different noisy labels levels show that the proposed method has robustness to noise and significantly surpasses other approaches, which provides an important reference value for accurate fault diagnosis for rotating equipment parts with noisy labels.