Conventional Retrieval-Augmented Generation (RAG) systems often struggle with complex multi-hop queries over long documents due to their single-pass retrieval. We introduce MM-Doc-R1, a novel framework that employs an agentic, vision-aware workflow to address long document visual question answering through iterative information discovery and synthesis. To incentivize the information seeking capabilities of our agents, we propose Similarity-based Policy Optimization (SPO), addressing baseline estimation bias in existing multi-turn reinforcement learning (RL) algorithms like GRPO. Our core insight is that in multi-turn RL, the more semantically similar two trajectories are, the more accurate their shared baseline estimation becomes. Leveraging this, SPO calculates a more precise baseline by similarity-weighted averaging of rewards across multiple trajectories, unlike GRPO which inappropriately applies the initial state's baseline to all intermediate states. This provides a more stable and accurate learning signal for our agents, leading to superior training performance that surpasses GRPO. Our experiments on the MMLongbench-Doc benchmark show that MM-Doc-R1 outperforms previous baselines by 10.4%. Furthermore, SPO demonstrates superior performance over GRPO, boosting results by 5.0% with Qwen3-8B and 6.1% with Qwen3-4B. These results highlight the effectiveness of our integrated framework and novel training algorithm in advancing the state-of-the-art for complex, long-document visual question answering.