This study demonstrates the feasibility of producing three polysaccharides (neutral LJP -1, acidic LJP-2 and acidic LJP-3) with significant in vitro and in vivo anti-inflammatory activities from the flowers of Lonicera japonica. The three polysaccharides differed in chemical composition, molecular weight (M_w) distribution, glycosidic linkage pattern, functional groups and morphology. They exhibited excellent protective effects (in a dose-dependent manner) in lipopolysaccharide-injured RAW264.7 macrophages and CuSO₄-damaged zebrafish via reducing NO production and inhibiting the overexpressions of inflammation-related transcription factors, inflammatory proteins and cytokines in the NF-κB/MAPK signaling pathways. Their anti-inflammatory effects varied owing to their different molecular characteristics and chemical compositions. Overall, LJP-2 at 400 μg/mL was the most effective. LJP-2 consisted mainly of →5)-α-L-Araf (1→, →4)-α-L-GalpA (1→ and →2)-α-L-Rhap (1→ residues with terminal T-β-D-Glcp. Thus, honeysuckle flowers are good sources of anti-inflammatory polysaccharides, and precise fractionation enables the production of potent anti-inflammatory agents for the development of functional foods and healthcare products.