HMGR is a crucial enzyme in the biosynthesis of terpenoids. We cloned FaHMGR and found that FaHMGR expression in fruit was significantly higher than other tissues, especially during the coloring stage. Suppression of FaHMGR (FaHMGRR) promoted coloration by increasing anthocyanin content and produced five new components. In contrast, FaHMGR overexpression (FaHMGROE) downregulated most anthocyanin genes and reduced hexanoic acid methyl ester and linalool contents, thereby inhibiting coloring. Transcriptomic and metabolomic analyses showed that DEGs in HMGROE vs. HMGRC (pCAMBIA1302 empty vector transformant serving as a control) were significantly enriched in phenylpropanoid biosynthesis pathway and pathways related to terpenoid metabolism and MeJA, suggesting MeJA as a potential mediator of HMGR's influence on terpenoid pathways. Additionally, DEGs in HMGRR vs. HMGRC were enriched in anthocyanin biosynthesis, particularly keracyanin and pelargonidin, which may explain the promoted coloration observed in HMGRR. WGCNA analysis identified five module genes with distinct expression patterns in HMGRR and HMGROE, including ERF118 and WRKY12, which may impact fruit quality by regulating HMGR activity.