Document understanding and analysis have received a lot of attention due to their widespread application. However, existing document analysis solutions, such as document layout analysis and key information extraction, are only suitable for fixed category definitions and granularities, and cannot achieve flexible applications customized by users. Therefore, this paper defines a new task named ``Class-Agnostic Region-of-Interest Matching'' (``RoI-Matching'' for short), which aims to match the customized regions in a flexible, efficient, multi-granularity, and open-set manner. The visual prompt of the reference document and target document images are fed into our model, while the output is the corresponding bounding boxes in the target document images. To meet the above requirements, we construct a benchmark RoI-Matching-Bench, which sets three levels of difficulties following real-world conditions, and propose the macro and micro metrics to evaluate. Furthermore, we also propose a new framework RoI-Matcher, which employs a siamese network to extract multi-level features both in the reference and target domains, and cross-attention layers to integrate and align similar semantics in different domains. Experiments show that our method with a simple procedure is effective on RoI-Matching-Bench, and serves as the baseline for further research. The code is available at https://github.com/pd162/RoI-Matching.