Codes serve as the fundamental language for human to communicate with machines, and various Transformer-based models are trained to process codes in recent advancements. A unique symmetry of code is its semantic-preserving permutation, which allows certain lines to be rearranged without altering the overall meaning. To capture such symmetry, we propose a novel attention mechanism that incorporates semantic-preserving permutation equivariance, called the SPE attention. By leveraging the symmetry relationships within code, we introduce a directed layered graph to represent the code structure, and this graph is then summarized into a symmetry mask. The SPE attention integrates those symmetry masks, granting semantic-preserving permutations equivariance to the model. Experiments on various code related tasks, including code summarization and error detection, demonstrate the effectiveness of the proposed SPE attention.