Scientific reasoning is a key aspect of human intelligence, requiring the integration of multimodal inputs, domain expertise, and multi-step inference across various subjects. Existing benchmarks for multimodal large language models (MLLMs) often fail to capture the complexity and traceability of reasoning processes necessary for rigorous evaluation. To fill this gap, we introduce SciVQR, a multimodal benchmark covering 54 subfields in mathematics, physics, chemistry, geography, astronomy, and biology. SciVQR includes domain-specific visuals, such as equations, charts, and diagrams, and challenges models to combine visual comprehension with reasoning. The tasks range from basic factual recall to complex, multi-step inferences, with 46% including expert-authored solutions. SciVQR not only evaluates final answers but also examines the reasoning process, providing insights into how models reach their conclusions. Our evaluation of leading MLLMs, including both proprietary and open-source models, reveals significant limitations in handling complex multimodal reasoning tasks, underscoring the need for improved multi-step reasoning and better integration of interdisciplinary knowledge in advancing MLLMs toward true scientific intelligence. The dataset and evaluation code are publicly available at https://github.com/CASIA-IVA-Lab/SciVQR.

We present M³-VQA, a novel knowledge-based Visual Question Answering (VQA) benchmark, to enhance the evaluation of multimodal large language models (MLLMs) in fine-grained multimodal entity understanding and complex multi-hop reasoning. Unlike existing VQA datasets that focus on coarse-grained categories and simple reasoning over single entities, M³-VQA introduces diverse multi-entity questions involving multiple distinct entities from both visual and textual sources. It requires models to perform both sequential and parallel multi-hop reasoning across multiple documents, supported by traceable, detailed evidence and a curated multimodal knowledge base. We evaluate 16 leading MLLMs under three settings: without external knowledge, with gold evidence, and with retrieval-augmented input. The poor results reveal significant challenges for MLLMs in knowledge acquisition and reasoning. Models perform poorly without external information but improve markedly when provided with precise evidence. Furthermore, reasoning-aware agentic retrieval surpasses heuristic methods, highlighting the importance of structured reasoning for complex multimodal understanding. M³-VQA presents a more challenging evaluation for advancing the multimodal reasoning capabilities of MLLMs. Our code and dataset are available at https://github.com/CASIA-IVA-Lab/M3VQA.