The invention relates to a flexible MEMS electric double layer capacitor pressure sensor and a preparation method thereof, wherein the sensor comprises a micro cavity, a measuring electrode, a reference electrode and a lead wire; a capacitance formed by positive and negative ion layers of the contact surface of the reference electrode or the measuring electrode with the electrolyte solution is called as an electric double layer capacitor; and the change of the contact area of the electrolyte solution with the measuring electrode is called as the change of the electric double layer capacitancevalue. By using the electric double layer capacitor to measure a pressure value and a change amount of the liquid environment, the volume of the electrolyte solution entering the micro cavity changeswith the volume of the micro bubble in the micro cavity when the pressure of the liquid environment changes, thereby measuring the volume change of the electrolyte solution entering the micro cavity so as to obtain the environmental pressure. The invention has the advantages of compact structure, small size, high sensitivity, simple process and good biocompatibility, and can be used for pressure measurement in the implant.