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In this study, the structure-activity relationship of finger citron polysaccharides (FCPs) and their phosphorylated derivatives (P-FCPs) was investigated. Three FCPs (FCP20, FCP40 and FCP60) were successively fractionated by ethanol, and were phosphorylated modification to obtain P-FCPs (P-FCP20, P-FCP40 and P-FCP60). FCPs and P-FCPs are acidic heteropolysaccharides composed of mannose, rhamnose, glucose, galactose, arabinose and galacturonic acid, and exhibited different content of neutral sugar, uronic acid, proteins, polyphenols and sulfates. FTIR and NMR analyses determined the structures of FCPs and P-FCPs, indicating that the phosphorylation modification was successful. P-FCPs possessed the smaller molecular weight distribution and particle size, with significant changes in microstructure than FCPs. Additionally, P-FCPs showed significantly increased antioxidant and α-amylase inhibitory activities compared to FCPs. The inhibitory mechanisms of FCP40 and P-FCP40 on α-amylase was a mixed-type manner and dynamic fluorescence quenching. The results demonstrate that phosphorylation modification can alter the structural features and bioactivities of FCPs, providing an approach for the further development of finger citron in the field of medicinal and functional foods.