The invention discloses a method for high-throughput analysis of plant secondary metabolites based on LCMS. A Scheduled-MRM mode is adopted to realize one-needle sample injection within 45min. Meanwhile, 130 types of plant secondary metabolites including anthocyanidin, benzoic acid and derivatives thereof, catechin and derivatives thereof, coumarin and derivatives thereof, dihydrochalcone, flavanone, flavone, flavonol, isoflavone, phenylpropanoids, procyanidine, stilbene, terpenes and the like are subjected to high-throughput absolute quantitative analysis. The method is high in pretreatment extraction efficiency, an instrument analysis method is wide in linear range, and high-abundance and low-abundance secondary metabolites with a large content difference can be detected and analyzed atthe same time; linear correlation is good, and a correlation coefficients are all higher than 0.995; the quantification limit of partial substances is as low as 0.01 ng/mL, and the sensitivity of themethod is high; accuracy is 80.2%-118.2%, and precision is 0.7%-119.9%; and high throughput and method sensitivity can be considered through Scheduled-MRM scanning, and the method can be widely applied to analysis of secondary metabolites in different complex plant samples.