Commit messages record code changes (e.g., feature modifications and bug repairs) in natural language, and are useful for program comprehension. Due to the frequent updates of software and time cost, developers are generally unmotivated to write commit messages for code changes. Therefore, automating the message writing process is necessitated. Previous studies on commit message generation have been benefited from generation models or retrieval models, but the code structure of changed code, i.e., AST, which can be important for capturing code semantics, has not been explicitly involved. Moreover, although generation models have the advantages of synthesizing commit messages for new code changes, they are not easy to bridge the semantic gap between code and natural languages which could be mitigated by retrieval models. In this paper, we propose a novel commit message generation model, named ATOM, which explicitly incorporates the abstract syntax tree for representing code changes and integrates both retrieved and generated messages through hybrid ranking. Specifically, the hybrid ranking module can prioritize the most accurate message from both retrieved and generated messages regarding one code change. We evaluate the proposed model ATOM on our dataset crawled from 56 popular Java repositories. Experimental results demonstrate that ATOM increases the state-of-the-art models by 30.72% in terms of BLEU-4 (an accuracy measure that is widely used to evaluate text generation systems). Qualitative analysis also demonstrates the effectiveness of ATOM in generating accurate code commit messages.