Molecularly imprinted polymers prepared using traditional functional monomers and cross-linkers exhibit slow binding kinetics, low electrocatalytic activity and adsorption capacity. Herein, we report a new composite of ionic liquid-based graphene and molecularly imprinted polymer (IL-GR-MIP) with high electrocatalytic activity and adsorption capacity to construct an effective electrochemical sensor for 6-benzylaminopurine (6-BAP). Our objective was to enhance the efficiency of the sensor by incorporating more IL in the MIP framework. We synthesized IL-GR-MIP using ionic liquid 1-vinyl-3-butylimidazolium tetrafluoroborate (IL) as functional monomer, ionic liquid 1,4-butanediyl-3,3'-bis-l-vinylimidazolium dibromide (IL) as cross-linker, 6-BAP as template, and GR as supporter. IL-GR-MIP was characterized by Fourier transform infrared spectroscopy, thermal gravimetric analysis, Raman spectroscopy, X-ray photoelectron spectroscopy, and scanning electron microscope. Compared with GR-MIP composites based on methacrylic acid or IL as functional monomer, N, N'-methylenebisacrylamide and ethylene glycol dimethacrylate as cross-linker, the IL-GR-MIP (prepared with ionic liquids as functional monomer and cross-linker) sensor exhibited highest peak current for 6-BAP. The results indicate the ability of IL as cross-linker to enhance electrocatalytic activity and adsorption capacity for 6-BAP of IL-GR-MIP. Under the optimized conditions, the peak current of IL-GR-MIP sensor was linear to 6-BAP concentration in the range of 0.5-50 μM with a detection limit of 0.2 μM (S/N = 3). The IL-GR-MIP sensor exhibited good selectivity with the anti-interference ability of 1000-fold ascorbic acid in 6-BAP determination. Furthermore, we demonstrated practical applicability of IL-GR-MIP sensor in detecting 6-BAP in real samples with satisfactory results.