With the blossom of deep learning models and services, it has become an imperative concern to safeguard the valuable model parameters from being stolen. Watermarking is considered an important tool for ownership verification. However, current watermarking schemes are customized for different models and tasks, hard to be integrated as an integrated intellectual protection service. We propose Hufu, a modality-agnostic watermarking system for pre-trained Transformer-based models, relying on the permutation equivariance property of Transformers. Hufu embeds watermark by fine-tuning the pre-trained model on a set of data samples specifically permuted, and the embedded model essentially contains two sets of weights -- one for normal use and the other for watermark extraction which is triggered on permuted inputs. The permutation equivariance ensures minimal interference between these two sets of model weights and thus high fidelity on downstream tasks. Since our method only depends on the model itself, it is naturally modality-agnostic, task-independent, and trigger-sample-free. Extensive experiments on the state-of-the-art vision Transformers, BERT, and GPT2 have demonstrated Hufu's superiority in meeting watermarking requirements including effectiveness, efficiency, fidelity, and robustness, showing its great potential to be deployed as a uniform ownership verification service for various Transformers.