In a realistic dialogue system, the input information from users is often subject to various types of input perturbations, which affects the slot-filling task. Although rule-based data augmentation methods have achieved satisfactory results, they fail to exhibit the desired generalization when faced with unknown noise disturbances. In this study, we address the challenges posed by input perturbations in slot filling by proposing Noise-BERT, a unified Perturbation-Robust Framework with Noise Alignment Pre-training. Our framework incorporates two Noise Alignment Pre-training tasks: Slot Masked Prediction and Sentence Noisiness Discrimination, aiming to guide the pre-trained language model in capturing accurate slot information and noise distribution. During fine-tuning, we employ a contrastive learning loss to enhance the semantic representation of entities and labels. Additionally, we introduce an adversarial attack training strategy to improve the model's robustness. Experimental results demonstrate the superiority of our proposed approach over state-of-the-art models, and further analysis confirms its effectiveness and generalization ability.