A molecularly imprinted electrochemiluminescence sensor for detection of cinchonine based on surface self-assembly of molecularly imprinted membrane on magnetic nanoparticles was developed. Cinchonine was used as template and lauryl mercaptan was used as assembling monomer. The morphology and particle size distribution of the magnetic nanoparticles were characterized by TEM, and the infrared spectroscopy was used to study the structure and composition of cinchonine, molecularly imprinted membrane before and after elution. The results showed that, cinchonine could be specifically assayed with a linear relationship between the signal intensity and the logarithm of concentrations of cinchonine in the range of 1×10-10 mol/L to 9×10-8 mol/L. The detection limit for cinchonine was 3. 5×10-11mol/L. The sensor was used for the determination of cinchonine in serum samples, with the recoveries of 98. 8% to 104. 7%.