Neuron-on-a-chip is a neuron based cell chip providing multichannel electrical signal recording through a microelectrode array (MEA) from live in vitro neurons and it is widely applied in a neuronal network study, a biological processor and a cell-based biosensor. In neuron-on-a-chip technology, there are two big problems: 1) Many MEAs are required for statistical analysis, 2) Neurons migrate from their initial position and it weakens neuron-electrode coupling. In this work, to solve the problems, agarose hydrogel is used as a cell repulsive background material or 3D cell scaffold material. Based on the properties of agarose hydrogel, we developed two kinds of agarose hydrogel based neuron patterning technique and applied them to neuron-on-a-chip technology for solving mentioned problems. 1) independent neuronal circuit array on a chip for high throughput electrophysiological screening, 2) entrapped neuron array for positioning and immobilizing neurons. Independent neuronal circuit array on a chip is capable of measuring electrophysiological signals from tens of independent micro neuronal circuits simultaneously. Agarose hydrogel is fabricated as an array of microwells and it isolates and confines micro neuronal circuits. Recorded extracellular spikes from discrete neuronal circuit array are independent and bursts are asynchronous, so it makes possible obtain tens of data points from single MEA. Entrapped neuron array offers selective patterning of cell body and immobilizing neurons. Neurons are mixed in agarose hydrogel and the neuron/agarose hydrogel is fabricated as an array of micro spots. Neuron entrapped agarose hydrogel cannot move its soma but it freely spreads out its neurite along the cell adhesive protein on MEA surface and forms a neuronal network. These two types of neuron array present a new paradigm for neuron-on-a-chip like high throughput electrophysiological screening systems and in vitro neuronal circuit design capability.