The yield and quality of crops are the foundation of sustainable agriculture, which can be affected by plant health and environmental factors. Plant metabolism runs through the whole life process of plants, in which primary metabolism can directly affect the growth and development of crops, thereby affecting crop yields. The secondary metabolism is more involved in the interaction between plants and the environment. Secondary metabolism production provides plants with on-demand biochemical capabilities to cope with highly unpredictable fluctuations of biotic and abiotic stress conditions. Therefore, secondary metabolism is also crucial for plant growth and development. In addition, some secondary metabolites in crops are also nutrients, functional and pharmacological components, which can affect the quality of crops. By analyzing plant metabolism, we can analyze the formation mechanism of plant yield and quality, and then make appropriate adjustments to obtain the products we want, which is of great benefit to the sustainable development of agriculture.