Local electrodeposition by using a micropipette is a potential method for fabrication of 3D metallic micro/nano-structures by confining the electrochemical reaction in a liquid meniscus, which is formed between the nozzle of the micropipette and a substrate. One of the key problems associated with this method is the nozzle clogging due to the small size of the micropipette, where the nozzle aperture is on the order of 1 μm and the fast speed of electrochemical reaction. This paper presents a method for resolving the nozzle clogging problem inherently with the local electrodeposition of microstructures. The reason of micrometric nozzle clogging was firstly investigated. A new method by relieving the nozzle deformation as well as adjusting the liquid meniscus bridge during the electrodeposition procedure was proposed. Through this way, electrodeposition of microstructures could thus be carried out with a high reproductivity without influences of the nozzle clogging. Experiments were carried out to demonstrate the feasibility of the method. It is proved that the reproductivity, the nozzle condition, as well as the surface quality of the microstructures in local electrodeposition could be improved based on the proposed method.