The manipulation of conductive nanowires (NWs) on semiconductor platforms provides important insights into the fabrication of nanoscale electronic devices. In this work, we directly observed the electric field-induced phase transitions in atomic Au-NWs self-assembled on Ge(001) surfaces using scanning tunneling microscopy (STM). The tunneling electrons and electric fields underneath a STM tip apex can effectively trigger a phase transition in Au-NWs on Ge(001) surfaces. Such phase transitions are associated with a remarkable atomic rearrangement in the Au-NWs, thereby modifying their band structures. Moreover, directly monitoring the dynamic reconstruction of Au-NWs on Ge(001) surfaces helps us to understand the NWs' intricate atomic configurations and their electronic properties. The spatially controlled phase transition at the nanometer scale using STM shows the possibility of modulating NWs' properties at an atomic scale.