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Applying the knowledge of an object detector trained on a specific domain directly onto a new domain is risky, as the gap between two domains can severely degrade model's performance. Furthermore, since different instances commonly embody distinct modal information in object detection scenario, the feature alignment of source and target domain is hard to be realized. To mitigate these problems, we propose a Graph-induced Prototype Alignment (GPA) framework to seek for category-level domain alignment via elaborate prototype representations. In the nutshell, more precise instance-level features are obtained through graph-based information propagation among region proposals, and, on such basis, the prototype representation of each class is derived for category-level domain alignment. In addition, in order to alleviate the negative effect of class-imbalance on domain adaptation, we design a Class-reweighted Contrastive Loss to harmonize the adaptation training process. Combining with Faster R-CNN, the proposed framework conducts feature alignment in a two-stage manner. Comprehensive results on various cross-domain detection tasks demonstrate that our approach outperforms existing methods with a remarkable margin. Our code is available at https://github.com/ChrisAllenMing/GPA-detection.