Citrus fruits are rich sources of different phytochemicals for human health due to their high anti-oxidant capacity. However, the anti-aging effect of citrus fruits has not been well understood. In this study, methanol extracts taken at various developmental stages from tissues of Citrus unshiu was used to investigate its anti-aging effect by an elastase/collagenase inhibition assay, and a gas chromatography-mass spectrometry (GC-MS) analysis was carried out to identify the potential anti-aging compositions. The elastase/collagenase inhibitory activity was greatest in the flesh of immature green fruit (i.e., early July flesh (EJF)), and four candidate compounds were selected by GC-MS and evaluated by a collagenase inhibition assay. Three of the four candidate compounds (heptadecanoic acid, D-allose, and 5-hydroxymethyl-2-furaldehyde (HMF)) showed anti-aging activity, and the activity was highest in heptadecanoic acid, followed by D-allose and HMF. The total phenolic content (TPC), total flavonoid content (TFC), and anti-oxidant activity (DPPH and ferric reducing anti-oxidant power (FRAP) assay) were also investigated. Interestingly, the patterns of the total phenolic/flavonoid content and the anti-oxidant activity were different from that of the elastase/collagenase inhibitory activity. Flowers had the most anti-oxidant activity followed by immature fruit, and the fruit peels had more anti-oxidant activity than its flesh at all stages of development. This study demonstrated that the flesh of immature fruit and flowers of C. unshiu could be sources of anti-aging and anti-oxidant agents for human health, respectively.