Chitosan is the only cationic polysaccharide in nature. It is a type of renewable resource and is abundant. It has good biocompatibility, biodegradability and biological activity. The amino and hydroxyl groups in its molecules can be modified, which enables chitosan to contain a variety of functional groups, giving it a variety of properties. In recent years, researchers have used different strategies to synthesize a variety of chitosan derivatives with novel structure and unique activity. Structure combination is one of the main strategies. Therefore, we will evaluate the synthesis and agricultural antimicrobial applications of the active chitosan derivatives structure combinations, which have not been well-summarized. In addition, the advantages, challenges and developmental prospects of agricultural antimicrobial chitosan derivatives will be discussed.