Recent developments in large language models (LLMs) have led to significant improvements in intelligent dialogue systems'ability to handle complex inquiries. However, current LLMs still exhibit limitations in specialized domain knowledge, particularly in technical fields such as agriculture. To address this problem, we propose ShizishanGPT, an intelligent question answering system for agriculture based on the Retrieval Augmented Generation (RAG) framework and agent architecture. ShizishanGPT consists of five key modules: including a generic GPT-4 based module for answering general questions; a search engine module that compensates for the problem that the large language model's own knowledge cannot be updated in a timely manner; an agricultural knowledge graph module for providing domain facts; a retrieval module which uses RAG to supplement domain knowledge; and an agricultural agent module, which invokes specialized models for crop phenotype prediction, gene expression analysis, and so on. We evaluated the ShizishanGPT using a dataset containing 100 agricultural questions specially designed for this study. The experimental results show that the tool significantly outperforms general LLMs as it provides more accurate and detailed answers due to its modular design and integration of different domain knowledge sources. Our source code, dataset, and model weights are publicly available at https://github.com/Zaiwen/CropGPT.