Crop diseases can severely impact crop yield, quality, and economic benefits. The extensive use of chemical pesticides for disease control not only affects food safety and causes environmental pollution but also leads to the development of disease resistance, increasing the difficulty of disease management and severely affecting the development of agricultural production. Therefore, the search for more efficient and environmentally friendly pesticides is an urgent priority. Biopesticides, derived from natural products, have the advantages of high biological activity, environmental friendliness, and less likelihood of causing resistance in pests. They play an important role in the prevention and control of crop diseases, reduction of crop losses, safeguarding food security, and protection of the ecological environment. This article provides a comprehensive review of the mechanisms by which natural products act against fungal, bacterial, viral, and nematode diseases, as well as their application progress in the prevention and control of crop diseases. It also looks forward to their application prospects, which will provide a theoretical basis for the green prevention and control of crop diseases.