Microelectrode array (MEA) is one of the representative platforms for recording and stimulating neurons to explore their populational electrophysiological activities. Due to the layered structures of the nervous system, various three-dimensional (3D) MEAs have been used to reach specific target depths of neuronal tissues. But it is still difficult to monolithically fabricate various heights of microelectrodes, particularly with optical transparency. Here, we present a 3D MEA with different heights fabricated by multi-step silicon deep reactive ion etching. The microelectrodes were embedded in reflowed glass for high transparency which enables both neural tissue observation and optical stimulation. The heights of microelectrodes were well controlled by our fabrication processes and electrical connections were made with through glass vias (TGVs) to the bottom side for individual addressing. To confine electric stimulation in a small area, we used microelectrodes neighboring a stimulation electrode as local returns. The feasibility of the fabricated MEA was demonstrated by stimulating the mouse retina and successfully recording spikes of ganglion cells located near the stimulation site. Consistent with our COMSOL simulation, the ex vivo experimental results showed the stimulation current confinement was effective. Our study provides a new tool for 3D nervous systems and its fabrication method.