In order to enable electrode sites to get closer to target neurons, obtain a better stimulation and minimize the electrochemical erosion of electrode, we proposed dome-shaped flexible neural microelectrode arrays (MEAs) for neural applications. With the use of photosensitive polyimide (Durimide 7510, PI) as substrate, a flexible microelectrode with 6 × 6 array of dome-shaped electrode sites was fabricated by combining photolithography and metal patterning with electroplating process. An evaluation of the dome-shaped electrode was also performed by simulation, SEM and impedance test. Experimental results showed, compared with conventional planar microelectrodes with the same base area, the 3D dome-shaped microelectrodes exhibited an 80% decrease in electrode impedance. The dome-shaped electrodes produce more uniform current distribution than the 3D pyramid-shaped microelectrode, which is helpful for its long-term safety of stimulation.