Citrus reticulata ‘Chachi’ (CRC), recognized for its considerable edible and medicinal significance, is a valuable source of metabolites beneficial to human health. This research investigates the metabolic distinctions and antioxidant properties across four different parts of CRC, using multivariate statistical analysis to interpret metabolomic data and network pharmacology to identify potential antioxidant targets and relevant signaling pathways. The results indicate considerable metabolic differences in different parts of the sample, with 1622 metabolites showing differential expression, including 816 secondary metabolites, primarily consisting of terpenoids (31.02%) and flavonoids (25.22%). The dried mature citrus peel (CP) section demonstrates the highest level of total phenolics (6.8 mg/g), followed by the pulp without seed (PU) (4.52 mg/g), pulp with seed (PWS) (4.26 mg/g), and the seed (SE) (2.16 mg/g). Interestingly, targeted high-performance liquid chromatography of flavonoids reveals the highest level of nobiletin and tangeretin in CP, whereas PU has the highest level of hesperidin, narirutin, and didymin. Furthermore, all four sections of CRC exhibit robust antioxidant properties in in vitro assessments (CP > PU > PWS > SE). Lastly, the network pharmacology uncovered potential antioxidant mechanisms in CRC. This research offers deeper insights into the development and utilization of byproducts in the CRC processing industry.