Abstract:  Novel five basic binuclear functional ionic liquids with an imidazolium structure were synthesized via a two step method and used as the catalyst in the preparation of biodiesel through transesterification from cottonseed oil. The ionic liquids exhibit good catalytic performances in the transesterification; among them, bis-(3-methyl-1-imidazolium-)-ethlyene dihydroxide performs best. Their catalytic activity is related to the lengths of the carbon chain in the cations. The influences of the catalyst dosage, reaction time and temperature, and the molar ratio of methanol to cottonseed oil on the transesterificaion were investigated. The fraction and selectivity of fatty acid methyl ester in the biodiesel product reach 98.5% and 99.9%, respectively, at 55℃ for 4h with a bis-(3-methyl-1-imidazolium-)-ethlyene dihydroxide catalyst dosage of 0.4% and methanol to cottonseed oil molar ratio of 12. The fraction of fatty acid methyl ester can be maintained at 96.2% with only little monoglycerides and diglycerides in the product after the catalyst is repeatedly used for 7 times, which implies that these bication ionic liquids with an imidazolium structure are suitable catalysts for the synthesis of biodiesel through transesterification.