Abstract: Microarrayer is the key instrument for biochip fabrication. The working process and system configuration of microarrayer were studied. Special attention was paid to the computation method of the microarrayer working path in biochip fabrication. On the condition of given parameters, such as sample variety, slip quantity, spot matrix module, pin matrix module etc., the working path was divided into two main sub-path, such as z axis pin path, xy axis spotting path. Then the tree classing method was taken to calculate the working path with the given parameters. The method and expressions were presented. The main factors for working path were analyzed. The agreement of the final computation results with the experimental data indicates this method can be used to estimate the working path of microarrayer quickly and effectively at engineering analyses. It has the significance for design of microarrayer and working path plan.