The effective management of low-concentration dye pollutants is a challenging task. Among various strategies, the Fenton reaction emerges as a powerful approach for the degradation of dyes, particularly in the presence of highly efficient catalysts. This study presents the utilization of antimony tungstate nests modified small magnetite nanospheres (Fe3O4/Sb2WO6) as a heterostructure catalyst for the photo-Fenton mineralization of low-concentration organic pollutants, exemplified by methylene Blue (MB) at ppm levels. The synthesis of Fe3O4/Sb2WO6 involves the in situ co-precipitation of agglomerated Fe3O4 nanospheres on hierarchial Sb2WO6 nests. The resulting Fe3O4/Sb2WO6 catalyst exhibits exceptional catalytic efficiency, demonstrating its capability to efficiently decontaminate low-concentration MB wastewater. Kinetic analyses reveal that the photo Fenton-like mineralization route adheres to the first-order reaction kinetic model, and approximately 100% mineralization of MB is achieved with a minimal catalyst amount of (4 mg/L). The straightforward preparation and outstanding performance of Fe3O4/Sb2WO6 position it as a promising candidate for the purification of dye pollutants.