Neurodegenerative diseases are associated with neuroinflammation, manifested by over-production of nitric oxide (NO) by microglial cells. Now there still lack effective treatment and prevention for the neurodegenerative diseases. Concerning neuroinflammation mediated by microglia cell, bioactivity-guided phytochemical research of Pongamia pinnata (L.) Pierre was performed in this study. A new chlorinated flavonoid, 2′,6′-dichlore-3′, 5′-dimethoxy-[2′′,3′′:7,8]-furanoflavone (1) was identified together with 29 known compounds, including flavonoids (compounds 2-17), isoflavonoids (compounds 18-23), chalcones (compounds 24-25), flavonones (compounds 26-27), triterpenes (28-29) and alkaloid (30) from the effective dichloride methane extract of dry stem of P. pinnata (L.) Pierre. Their structures were elucidated by physicochemical and spectral methods. The anti-neuroinflammatory activities were assayed in BV-2 cells by assessing LPS-induced NO production. Then pongaglabol methyl ether (2), lonchocarpin (24) and glabrachromene II (25) were selected as potential therapeutic agents for neurodegenerative diseases because of their significant anti-neuroinflammatory activities. Furthermore, the characteristics of structure type existing in P. pinnata (L.) Pierre and brief SAR were summarized, respectively.