Microelectrode arrays (MEAs) play a crucial role in investigating the electrophysiological activities of neuronal populations. Although two-dimensional neuronal cell cultures have predominated in neurophysiology in monitoring in-vitro the electrophysiological activity, recent research shifted toward culture using three-dimensional (3D) neuronal network structures for developing more sophisticated and realistic neuronal models. Nevertheless, many challenges remain in the electrophysiological analysis of 3D neuron cultures, among them the development of robust platforms for investigating the electrophysiological signal at multiple depths of the 3D neurons’ networks. While various 3D MEAs have been developed to probe specific depths within the layered nervous system, the fabrication of microelectrodes with different heights, capable of probing neural activity from the surface as well as from the different layers within the neural construct, remains challenging. This study presents a novel 3D MEA with microelectrodes of different heights, realized through a multi-stage mold-assisted electrodeposition process. Our pioneering platform allows meticulous control over the height of individual microelectrodes as well as the array topology, paving the way for the fabrication of 3D MEAs consisting of electrodes with multiple heights that could be tailored for specific applications and experiments. The device performance was characterized by measuring electrochemical impedance, and noise, and capturing spontaneous electrophysiological activity from neurospheroids derived from human induced pluripotent stem cells. These evaluations unequivocally validated the significant potential of our innovative multi-height 3D MEA as an avant-garde platform for in vitro 3D neuronal studies.