Abstract This study investigated the influence of rootstock selection on fruit quality dynamics during ripening in 'Wuming Orah' mandarin, establishing scientific criteria for optimal harvest time and ripening regulation. Using fragrant citrus (Citrus × junos Siebold ex Tanaka) and (Poncirus trifoliata (L.) Raf) as rootstocks, fruit samples were collected at eight developmental stages (S1–S8) spanning the color-break period to full maturity. Key quality parameters were analyzed, including color index of fruit pericarp, total soluble solids (TSS), titratable acidity (TA), juice rate, and primary metabolite profiles at five critical stages. Transcriptomic analysis via RNA-Seq was performed at three pivotal stages, with qRT-PCR validation of key genes. Results demonstrated that P. trifoliata-grafted fruits exhibited accelerated pericarp coloration and enhanced redness during S1–S5. Compared to C. junos-grafted fruits, P. trifoliata conferred significantly higher juice yield (increase: 0.37%–11.64%), TSS content (elevation: 0.73%–1.00%), and TSS/TA ratio (increase: 0.32–3.41). Sensory evaluation revealed superior overall preference scores for P. trifoliata fruits (8.11 vs. 7.22). Primary metabolomics analysis indicated elevated sucrose, D-fructose, D-glucose, and myo-inositol levels in P. trifoliata-grafted fruits. No significant inter-rootstock differences in TA, TSS/TA, or sensory attributes were observed during S6–S8. Transcriptomic profiling identified 1,481 differentially expressed genes, predominantly enriched in carbohydrate metabolism, protein phosphorylation, and transcriptional regulation pathways. qRT-PCR confirmed the early upregulation of CsSUC1 (the key sucrose transporter gene) in P. trifoliata-grafted fruits, correlating with accelerated sugar accumulation. These findings indicate that the optimal harvest window for P. trifoliata-grafted Wuming Orah mandarin occurs in early January—approximately two weeks earlier than C. junos-grafted fruits (mid-January). The hastened maturation associated with P. trifoliata rootstock appears mechanistically linked to enhanced soluble sugar accumulation.