Fertilizer application plays a crucial role in influencing the metabolites responsible for tea quality control. However, excessive chemical fertilizer application has detrimental effects on tea quality. To explore the influence of chemical and organic fertilizers on tea quality, a pot experiment was conducted with four treatments, including no fertilizer application as control, only chemical fertilizer (CF), only organic fertilizer (OF), and combined chemical fertilizer and organic fertilizers (CF + OF). Total polyphenol (TP), total amino acids (TAA), total flavonoids (TF), catechins and caffeine content, and total phenol-amino ratio (TP/TAA) and catechin astringency index (CAI) were analyzed to evaluate the tea quality, and try to reveal the regulating flavonoids pathway at gene expressional and transcriptomic levels. The results showed that, compared with control, all the fertilizer treatments increased significantly TF (19.70 %, 29.41 % and 64.56 % by CF, OF and CF + OF treatments, respectively) and TP contents (38.90 %, 27.19 % and 16.81 % by CF, OF and CF + OF treatments, respectively). OF and CF + OF treatments increased TAA (by 30.82 % and 38.92 %, respectively), and total catechins content (by 84.25 % and 60.39 %, respectively), while CF treatment decreased total catechins (by 6.83 %). As a result, CF treatment had lower CAI and higher TP/TAA; OF treatment had no effects on CAI and TP/TAA index; while CF + OF treatment had the highest tea quality with the lowest CAI and TP/TAA in the tea leaves. Fertilizers treatments affect flavonoids and catechins contents by regulating the phenylpropanoid and flavonoid biosynthesis pathways involved the modulation of structural genes, such as PAL, 4CL, C4H, and CHS. CF + OF treatment increased expression of genes, particularly DFR2, ANS3 and ANR2, which promoted the accumulation of (−)-epigallocatechin and (−)-epigallocatechin 3-gallate, ultimately increased total catechin content. This finding provides insight into the mechanisms underlying the effects of CF + OF promotes tea quality, and could provide scientific supports for tea cultivation and management.