Deep-narrow grooves (DNGs) of nickel-based alloy GH4169 are extensively used in aerospace industry. Electrochemical milling (EC-milling) can manufacture special structures including DNGs by controlling the moving path of simple tool, showing a flexible process with the advantages of high machining efficiency, regardless of material hardness, no residual stresses, burrs, and tool wear. However, due to the inefficient removal of electrolytic by-products in the inter-electrode gap (IEG), the machining accuracy and surface quality are always unsatisfactory. In this paper, a novel tube tool with wedged end face is designed to generate pulsating flow field in IEG, which can enhance the removal of electrolytic by-products as well as improve the machining quality of DNG. The flow field simulation results show that the electrolyte velocity in the IEG is changed periodically along with the rotation of the tube tool. The pulsating amplitude of electrolyte is changed by adjusting the wedged angle in the end face of the tube tool, which could affect the EC-milling process. Experimental results suggest that the machining quality of DNG, including the average width, taper of sidewall, and surface roughness, is significantly improved by using the tube tool with wedged end face. Compared with other wedged angles, the end face with the wedged angle of 40° is more suitable for the EC-milling process. DNG with the width of 1.49 mm ± 0.04 mm, taper of 1.53° ± 0.46°, and surface roughness (Ra) of 1.04 μm is well manufactured with the milling rate of 0.42 mm/min. Moreover, increasing the spindle speed and feed rate can further improve the machining quality of DNG. Finally, a complex DNG structure with the depth of 5 mm is well manufactured with the spindle speed of 4000 rpm and feed rate of 0.48 mm/min.