Retrieval-based multimodal document QA aims to identify and integrate relevant information from visually rich documents with complex multimodal structures. While retrieval-augmented generation (RAG) has shown strong performance in text-based QA, its extensions to multimodal documents remain underexplored and face significant limitations. Specifically, current approaches rely on query-agnostic document representations that overlook salient content and use static top-k evidence selection, which fails to adapt to the uncertain distribution of relevant information. To address these limitations, we propose the Multimodal Adaptive Retrieval-Augmented (MARA) framework, which introduces query-adaptive mechanisms to both retrieval and generation. MARA consists of two components: a Query-Aligned Region Encoder that builds multi-level document representations and reweights them based on query relevance to improve retrieval precision; and a Self-Reflective Evidence Controller that monitors evidence sufficiency during generation and adaptively incorporates content from lower-ranked sources using a sliding-window strategy. Experiments on six multimodal QA benchmarks demonstrate that MARA consistently improves retrieval relevance and answer quality over existing SOTA method.