MLLMs (Multimodal Large Language Models) have showcased remarkable capabilities, but their performance in high-stakes, domain-specific scenarios like surgical settings, remains largely under-explored. To address this gap, we develop \textbf{EyePCR}, a large-scale benchmark for ophthalmic surgery analysis, grounded in structured clinical knowledge to evaluate cognition across \textit{Perception}, \textit{Comprehension} and \textit{Reasoning}. EyePCR offers a richly annotated corpus with more than 210k VQAs, which cover 1048 fine-grained attributes for multi-view perception, medical knowledge graph of more than 25k triplets for comprehension, and four clinically grounded reasoning tasks. The rich annotations facilitate in-depth cognitive analysis, simulating how surgeons perceive visual cues and combine them with domain knowledge to make decisions, thus greatly improving models' cognitive ability. In particular, \textbf{EyePCR-MLLM}, a domain-adapted variant of Qwen2.5-VL-7B, achieves the highest accuracy on MCQs for \textit{Perception} among compared models and outperforms open-source models in \textit{Comprehension} and \textit{Reasoning}, rivalling commercial models like GPT-4.1. EyePCR reveals the limitations of existing MLLMs in surgical cognition and lays the foundation for benchmarking and enhancing clinical reliability of surgical video understanding models.