Persulfate activation has been applied as one of the efficient advanced oxidation processes (AOPs) to remediate polluted environments. In this study, a novel α-FeOOH anchored by graphene oxide (GO)-carbon nanotubes (CNTs) aerogel (α-FeOOH@GCA) nanocomposite activated persulfate system (α-FeOOH@GCA + KSO) was applied for decolorization of Orange II (OII). The decolorization of OII was remarkably enhanced to a level of 99% in this system compared with that of pristine α-FeOOH (44%) or GO-CNTs (~18%). The enhanced catalytic activity of α-FeOOH@GCA was due to the formation of a heterojunction by α-FeOOH and GO-CNTs as confirmed by the presence of Fe-O-C chemical bonds. The degradation intermediates of OII were comprehensively identified. The proposed degradation pathway of OII begins with the destruction of the conjugated structures of OII by the dominant reactive oxygen species, surface-bound SO. The decolorization efficiency of OII by the α-FeOOH@GCA activated persulfate system decreased from the first to third cycle of recycling. Ultraviolet (UV) irradiation or introduction of a small amount of Fe could restore the activation of this system. The results show that the α-FeOOH@GCA persulfate activation system promises to be a highly efficient environmental remediation method for organic pollutants.