3D aligned electrospun fibers hold a promising potential in a wide range of biomedical areas, including biosensors, controlled drug release, tissue engineering, etc. Thus, a cost-effective and easy way to scale-up fabrication for 3D aligned nanofibers is highly desired. Herein, a novel yet facile preparation process of 3D aligned nanofibers (3D AFs) by an improved electrospinning technique is reported. The obtained 3D AFs show enhanced controllability on morphology and fiber density, and thus facilitate adhesion and growth of human mesenchymal stem cells within their 3D nanofiber microarchitectures, leading to an excellent in vitro biocompatibility. Moreover, the 3D AFs with aligned morphology can enhance the neuron activities and induce directional cell growth along the direction of nanofiber orientation, thereby providing an excellent cue for the anchorage and migration dependent neurons. Combined with controllable morphology and structure, it is anticipated that this finding can lead to great applications of electrospun fibers in nerve tissue engineering, diagnostics, and other biomedical fields.