Flexible electrodes are extensively used to detect signals in electrocardiography, electroencephalography, electro-ophthalmography, and electromyography, among others. These electrodes can also be used in wearable and implantable medical systems. The collected signals directly affect doctors’ diagnoses of patient etiology and are closely associated with patients’ life safety. Electrodes with low contact impedance can acquire good quality signals. Herein, we established a method of arraying pyramidal microstructures on polydimethylsiloxane (PDMS) substrates to increase the contact area of electrodes, and a parylene transitional layer is coated between PDMS substrates and metal membranes to enhance the bonding force, finally reducing the impedance of flexible electrodes. Experimental results demonstrated that the proposed methods were effective. The contact area of the fabricated electrode increased by 18.15% per unit area, and the contact impedance at 20 Hz to 1 kHz scanning frequency ranged from 23 to 8 kΩ, which was always smaller than that of a commercial electrode. Overall, these results indicated the excellent performance of the fabricated electrode given its low contact impedance and good biocompatibility. This study can also serve as a reference for further electrode research and application in wearable and implantable medical systems.