The present invention provides a series of cyclin-dependent protein kinases (Cdks) inhibitors, Scutellaria flavonoid organic amine derivatives, synthesis and use thereof. The preparation method is as follows: taking Baicalein (or Wogonin) from Scutellaria baicalensis as lead compound, mixting it with formaldehyde solution and organic amine compounds based on the molar ratio of 1:1-1.2:1-1.2, adding methanol of duplicate weight than baicalein and reacting at 50-70° C., filtering the sediment and washing and then drying so as to get the product with a content of not less than 97% (weight). Similar to Flavopiridol and P276-00, the activity of baicalein organic amine derivatives inhibiting Cdks has an increase of 50 times compared with that of Baicalin. It can selectively induce apoptosis of the proliferative phase cancer cells, which has scarcely any influence to the normal structure, and it belongs to anticancer drugs of cell cycle inhibitor kind. The product has a rich source of raw materials and has simple process, high purity, low cost, clear metabolic mechanism, high efficiency and low toxicity, which can be made into oral preparations or injections together with acid salts and is expected to become high efficient and low toxicity anti-cancer and AIDS drugs.