The present work describes the in vitro aerosol deposition and enhanced deaggregation behavior of superparamagnetic iron oxide nanoaggregates (SPIONs). SPIONs were surface-coated with amine functionalized polyrotaxane and were proposed as a carrier for inhalation dry powders. Polyrotaxane is primarily composed of beta cyclodextrin rings which are spontaneously threaded on the block copolymer, poly(propylene glycol) bis(2-aminopropylether). Variable concentrations of surface coating polymers showed controlled manipulation of the crystal size and morphology. Magnetic nanoaggregates fabricated with low concentration of polyrotaxane showed cubic crystal morphology. However, these nanoaggregates exhibited rhombic dodecahedron crystal structure upon increasing the coating polymer concentration. In comparison to the spherical uncoated magnetic nanoparticles, cubic phase magnetic nanoaggregates demonstrated an enhanced in vitro aerosol deposition using magnetic field alignment. This enhancement can be accomplished at low inhalation flow rates (15 and 30 L/min). However, transformation to the cubic crystal structure was observed to be associated with a reduction in the powder geometric standard deviation. Using a mathematical modeling approach, we noted significant enhancement in the deaggregation behavior of inhalation dry powders; that can be achieved with small amounts of magnetic nanoaggregates. Aggregates of cubic nanoparticles showed promise for targeted pulmonary deposition of anticancer drugs.