A highly sensitive and high selective sensor which can detect drug molecules in a liquid environment was explored. By combining the Molecular Imprinting Technique (MIT), Film Bulk Acoustic Resonator (FBAR) and the micro fluidic technology, the new sensor was constructed. The preparing principle of adsorption layer materials for FBAR by the MIT was introduced and the Imprinting material with special adsorption properties for the special drug was developed by the MIT. Then, the material was coated on a FBAR as a adsorption layer based on a Micro-electrical-mechanical System and the micro fluidic technology. According to the piezoelectric equation and dynamic equation, the input impedance formulas of the equivalent circuit and electric port for the FBAR piezoelectric vibrator were derived. Furthermore, a model of the micro fluidic system with the MIT plus FBAR-based drug detection sensor was designed and a detailed theoretical derivation and analysis was performed. Finally, the sensor model was simulated using practical operating parameters. The results show that the quality of the mass loudness per unit area of the sensor is up to 0.8 pg/Hz·cm2, which is much higher than the quality of a conventional Quartz Crystal Microbalance (QCM) sensor. This advantage can greatly enhance the performance of the sensor for drug detection in the liquid environment.