While Multimodal Large Language Models (MLLMs) are advancing rapidly, accurately evaluating their capabilities remains challenging. Current paradigms primarily rely on holistic scoring and static leaderboards, which fail to disentangle fine-grained competencies. Specifically, they suffer from “Outcome Bias” by validating only final answers and ignoring intermediate reasoning. To address these limitations, we introduce ATOM (AnaTomy Of MLLM), a novel MLLM-as-a-judge framework designed to shift the focus from ranking to fine-grained diagnosis. ATOM decomposes complex reasoning into atomic criteria anchored in visual elements, enforcing verification against explicit visual facts. Validated on a newly constructed benchmark with rigorous human rankings, ATOM achieves state-of-the-art accuracy, surpassing the strongest baseline by up to 7.92%. Moving beyond ranking, ATOM bridges the gap between assessment and alignment: by pinpointing atomic-level failures, it establishes a closed-loop mechanism for targeted self-correction. This approach enables models to identify and rectify errors autonomously, successfully resolving up to 39.95% of previously failed queries without human intervention.