This study systematically measured and evaluated the active components in different organs of Chrysanthemum morifolium cv. Fubaiju at different harvesting stages to effectively utilize its non-medicinal parts for the comprehensive development and utilization of chrysanthemum resources. Simultaneously, its in vitro antioxidant capacity was evaluated using three antioxidant indicators: 1,1-dipheny l-2-trinitrophenylhydrazine (DPPH) radical-scavenging capacity, 2′-bis(3-ethylbenzene and thiazolin-6-sulfonic acid) diamine salt (ABTS) radical-scavenging capacity, and ferric-reducing antioxidant power (FRAP). The results showed that different organs of C. morifolium contain 9.13~52.18 mg/g crude fat, 62.72~189.50 mg/g protein, 138.26~459.12 mg/g crude fiber, 8.19~45.32 mg/g total amino acids, 0.45~4.6 mg/g essential amino acids, 11.86~80.99 mg/g total flavonoids, 13.11~99.33 mg/g total phenols, 20.24~96.78 mg/g neutral polysaccharides, and 9.46~43.28 mg/g acidic polysaccharides. Amino acid profiling further showed they contain 41.78~56.19% taste-related amino acids and 12.50~46.72% medicinal amino acids. Analysis of nine polyphenolic monomers showed that the phenolic acid compound content was significantly higher than the flavonoid compound content. A comprehensive analysis of the active components using principal component analysis and fuzzy mathematical membership function method ranked the plant organs as follows: seedlings (0.814), leaves (0.522), flowers (0.378), and stems (0.058). The overall antioxidant activities were ranked as follows: seedlings (65.76%), leaves (64.56%), flowers (62.53%), and stems (61.91%). In summary, the results provide strong scientific and technological support for the application of non-medicinal parts of Fubaiju, thereby expanding its application.