With the increasing application of three-dimensional pure aluminum microstructures in micro-electromechanical systems (MEMS) and for fabricating terahertz components, high-quality micro-shaping of pure aluminum has gradually attracted attention. Recently, high-quality three-dimensional microstructures of pure aluminum with a short machining path have been obtained through wire electrochemical micromachining (WECMM), owing to its sub-micrometer-scale machining precision. However, machining accuracy and stability decrease owing to the adhesion of insoluble products on the surface of the wire electrode in long-duration WECMM, which limits the application of pure aluminum microstructures with a long machining path. In this study, the bipolar nanosecond pulses are used to improve the machining accuracy and stability in long-duration WECMM of pure aluminum. A negative voltage of −0.5 V was considered appropriate based on experimental results. Compared with the traditional WECMM using unipolar pulses, the machining accuracy of the machined micro-slit and the duration of stable machining were significantly improved in long-duration WECMM using bipolar nanosecond pulses.