A series of NH2-functionalized nano-sized magnetic metal-organic frameworks (MOFs) were prepared in this study for Cr(VI) removal from wastewater. It was observed that not only the morphological, i.e., orientation growth of N-doped and iron-based metal-organic frameworks, but also the adsorption of magnetic MOFs is largely related to the used amount of ammonium hydroxide in preparation. For example, with increasing amounts of ammonium hydroxide used in preparation, the morphology of magnetic MOFs changed from spherical to cube and triangular cone. Moreover, the maximum adsorption capacity of spherical-magnetic MOFs, cubic-magnetic MOFs and triangular cone-magnetic MOFs could be up to 204.08 mg/g, 232.56 mg/g and 270.27 mg/g, respectively. Under optimal conditions, the adsorption process of magnetic MOFs for Cr(VI) was consistent with the pseudo-second-order rate equation (R2 = 1) and Langmuir isotherm model (R2 > 0.99). Therefore, magnetic MOFs developed in this work offered a viable option for the removal of Cr(VI) from wastewater.