A novel perfluoroalkyl-containing quaternary ammonium salt was synthesized from N-methyl diethanolamine and perfluorinated hexyl ethyl iodide by microwave technique. The structure of the product was characterized by fourier transform infrared spectroscopy, mass spectrometry and nuclear magnetic resonance spectrum. The effect of solvent dosage, microwave power, reactant mole ratio and reaction time on reaction conversion rate were studied. The Central-Composite mathematical relational model between conversion rate of N-methyl diethanolamine and effect factors was established to optimize the synthesis technique of the product. The optimum synthesis conditions were as follow: perfluorinated hexyl ethyl iodide 0.015mol, N-methyl diethanolamine 0.01mol, solvent dosage 50wt%(10ml), microwave power 582.49 W, reaction time 2.5 h. Under the optimal condition, in a short reaction time, only 10.42% of the conventional heating time, the conversion rate of MDEA was 89.15%.