We report the controlled synthesis of iron oxide microcubes (IOMCs) through the self-assembly arrays of ferric oxide hydroxide nanorods (NRs). The formation of IOMCs involves a complex interplay of nucleation, self-assembly, and growth mechanisms influenced by time, thermal treatment, and surfactant dynamics. The self-assembly of vertically aligned NRs into IOMCs is controlled by dynamic magnetism properties and capping agents like cetyltrimethylammonium bromide (CTAB), whose concentration and temperature modulation dictate growth kinetics and structural uniformity. These controlled structural growths were obtained via a hydrothermal process at 120 °C at various intervals of 8, 16, 24, and 32 h in the presence of CTAB as the capping agent. In this hydrothermal method, the formation of vertically oriented NR arrays was observed without the presence of ligands, binders, harsh drying techniques, and solvent evaporation. The formation of the self-assembly of NRs to IOMCs is obtained with an increase in saturated magnetization to attain the most stable state. The synthesized IOMCs have a uniform size, quasi-shape, and excellent dispersion. Due to its excellent magnetic and catalytic properties, IOMCs were employed to remove the various emerging pollutants known as per- and polyfluorinated substances (PFAS). Various microscopic and spectroscopic techniques were employed for the characterization and interaction studies of IOMCs with various PFAS. The interaction between IOMCs and perfluoroalkyl substances (PFAS) was investigated, revealing strong adsorption tendencies facilitated by electrostatic interactions, as evidenced by UV-vis and FT-IR spectroscopic studies. Furthermore, the higher magnetic and positive surface charge of IOMCs is responsible for an effective remediation eliminating any secondary pollution with ease of recovery after the sorption interaction studies, thereby making it practically worthwhile.