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Multi-modal Large Language Models (MLLMs) integrating images, text, and speech can provide farmers with accurate diagnoses and treatment of pests and diseases, enhancing agricultural efficiency and sustainability. However, existing benchmarks lack comprehensive evaluations, particularly in multi-level reasoning, making it challenging to identify model limitations. To address this issue, we introduce Agri-CM3, an expert-validated benchmark assessing MLLMs’ understanding and reasoning in agricultural management. It includes 3,939 images and 15,901 multi-level multiple-choice questions with detailed explanations. Evaluations of 45 MLLMs reveal significant gaps. Even GPT-4o achieves only 63.64% accuracy, falling short in fine-grained reasoning tasks. Analysis across three reasoning levels and seven compositional abilities highlights key challenges in accuracy and cognitive understanding. Our study provides insights for advancing MLLMs in agricultural management, driving their development and application. Code and data are available at https://github.com/HIT-Kwoo/Agri-CM3.