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Transformer-based models have demonstrated state-of-the-art performance in many intelligent coding tasks such as code comment generation and code completion. Previous studies show that deep learning models are sensitive to the input variations, but few studies have systematically studied the robustness of Transformer under perturbed input code. In this work, we empirically study the effect of semantic-preserving code transformation on the performance of Transformer. Specifically, 24 and 27 code transformation strategies are implemented for two popular programming languages, Java and Python, respectively. For facilitating analysis, the strategies are grouped into five categories: block transformation, insertion/deletion transformation, grammatical statement transformation, grammatical token transformation, and identifier transformation. Experiments on three popular code intelligence tasks, including code completion, code summarization and code search, demonstrate insertion/deletion transformation and identifier transformation show the greatest impact on the performance of Transformer. Our results also suggest that Transformer based on abstract syntax trees (ASTs) shows more robust performance than the model based on only code sequence under most code transformations. Besides, the design of positional encoding can impact the robustness of Transformer under code transformation. Based on our findings, we distill some insights about the challenges and opportunities for Transformer-based code intelligence.