Tailoring the structure of nanocrystal superlattices is an important step toward controlled design of novel nanostructured materials and devices. We demonstrate how the long-range order and macroscopic dimensions of magnetic nanoparticle arrays can be controlled by the use of a modulated magnetic field. Inducing a dipolar attraction during the initial stage of the drying-mediated self-assembly process was sufficient to assemble the superparamagnetic oleate-capped maghemite nanocubes into large and defect-free superstructures with both translational and orientational order. The characteristic dimensions of the superlattice are controlled by the particle concentration as well as the duration of the applied magnetic field. The superparamagnetic maghemite nanocubes assemble into large and highly oriented thin arrays by applying the magnetic field perpendicular to the substrate surface only during the initial phase of drying-mediated self-assembly. Micrometer-sized and thick three-dimensional mesocrystals are obtained when the drying dispersion is subjected to an external magnetic field of moderate strength for the entire duration of the assembly process. The discovery of how translational and orientation order of nanocrystal superlattices can be induced by a temporal modulation of an anisotropic interparticle force offers new insight on the importance of the initial nucleation stage in the self-assembly process and suggests new routes for controlled self-assembly of dipolar nanocrystals.