In the intricate process of maskless localized electrodeposition (MLED) for fabricating three-dimensional microstructures, specifically nickel micro-columns with an aspect ratio of 7:1, magnetic fields of defined strength were employed, oriented both parallel and anti-parallel to the electric field. The aim was to achieve nanocrystalline microstructures and elevated deposition rates. A detailed comparative analysis was conducted to examine the volumetric deposition rate, surface morphology, and grain size of the MLED nickel crystal 3D microstructures, both in the absence and presence of the two magnetic field directions, facilitated by a self-assembled experimental setup. The results indicate that the anti-parallel magnetic field significantly boosts the volumetric deposition rate to a notable 19,050.65 μm3/s and refines the grain size, achieving an average size of 24.82 nm. Conversely, the parallel magnetic field is found to enhance the surface morphology of the MLED nickel crystal 3D microstructure.