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Pea-tea intercropping is an excellent cultivation method that can improve tea quality. However, the underlying mechanism is still unclear. The present study was aimed at elucidating the mechanism of the effect of pea-tea intercropping on tea quality through a high-throughput method. Transcriptome and metabolome analyses were conducted to identify the changes in gene expression and metabolites changes intercropping, respectively. In addition, the amino acids and catechins were detected using the LC-MS method and quantified absolutely. The results showed that total polyphenols and catechins decreased but amino acids increased in pea intercropped tea shoots. Correspondingly, genes related to amino acid metabolism and flavonoid biosynthesis were differentially expressed. For amino acid metabolism, 11 differentially expressed genes were identified, including 5 upregulated and 6 downregulated genes. Meanwhile, three genes involved in carbohydrate transport and metabolism were upregulated in pea intercropped tea plants. These genes were also involved in amino acid metabolism. For flavonoid biosynthesis, two downregulated genes were identified, which were the flavonol synthase and anthocyanidin synthase genes and followed a similar pattern to changes in catechins and polyphenols. These advances have opened new horizons for understanding the biochemical mechanisms of amino acids and flavonoids in improving tea quality in the pea-tea intercropping cultivation model.