To study the chemical composition and their anti-inflammatory activities of honeysuckle (Lonicera japonica Thunb.) roots, seventeen compounds were isolated from the roots of L. japonica Thunb. by various chromatography, including silica gel, Sephadex LH-20 and preparative HPLC. Their structures were identified by MS, IR, and nuclear magnetic resonance spectra, as 1-oxo-(1H)-cyclopenta[b]benzofuran-7-carbaldehyde (1), 4-hydroxycinnamic acid (2), chlorogenic acid (3), loganin aglycone (4), caffeic acid (5), secologanin dimethyl acetal (6), korolkoside (7), coniferin (8), sweroside (9), secoxyloganin (10), 5-O-caffeoylquinic acid (11), chlorogenic acid methyl ester (12), chlorogenic acid ethyl ester (13), 3,5-O-dicaffeoylquinic acid (14), 4,5-O-dicaffeoylquinic acid (15), grandifloroside (16), and 4,5-O-dicaffeoylquinic acid (17). Among those, compound 1 is a new compound, and compound 8 is found in L. japonica for the first time. Compounds 1, 3, 14-17 showed significant anti-inflammatory activities against macrophage in zebrafish.