The deep micro-hole structure has important applications in the fields of aerospace, precision mold, automotive industry and medical equipment. Plasma-assisted electrochemical machining (PA-ECM) is an important method for deep micro-hole fabrication. However, when the machining depth is >500 μm (depth to diameter ratio of about 1:1), the electrolyte is difficult to flow into the machining area (inter-electrode gap), which is easy to cause abnormal spark discharge and even short circuit, affecting the processing stability. In order to solve the problem of lack of electrolyte in the machining area, a plasma-assisted shaped tube electrochemical machining (PA-STEM) method was proposed in this paper. In PA-STEM, the current is mainly conductive through the electrolyte jet, and the electric field of the tube electrode end face and sidewall is shielded by the gas film/plasma film, so the machining accuracy would not deteriorate under high machining voltage. As a hot gas medium, plasma can create a machining environment similar to electrochemical jet machining (EJM), hence a small pit is left at the bottom of the micro-hole. The higher voltage makes the gas film and plasma film more dense, which is beneficial to improve the machining accuracy of micro-hole. The tube electrode feeding rate should not be too fast to avoid damage to the machined surface caused by high-energy spark discharge. At high pulse frequency and low electrolyte flow rate, the energy of plasma is more stable, and it is more suitable for high-quality micro-hole machining. Through the optimization of the process parameters, a deep micro-hole with inlet diameter of 980 μm, outlet diameter of 750 μm, depth of 5 mm was obtained, and the depth-to-diameter ratio of the micro-hole is 5.1:1. Moreover, there is no recast layer on the sidewall subsurface of the micro-hole.