Owing to the implementation of increasingly stringent water conservation policies and regulations, the pulp and paper mill industry must make increased efforts to meet the limits for pollutant emissions. The primary pretreatment and secondary biochemical treatment methods used currently generally fail to meet the country-specific environmental regulations, and the wastewater must be processed further even after being subjected to secondary biochemical treatments. In this work, we synthesized Fe3O4/MnO2 nanocomposites (FMNs) with a flower-like structure for use in the heterogeneous photocatalytic treatment of biotreated papermaking wastewater. FMNs1.25, which were formed using a KMnO4/Fe3O4 molar ratio of 1.25, could be separated readily using an external magnetic field and exhibited higher photocatalytic activity than those of the other samples as well as MnO2 and Fe3O4. The effects of various experimental parameters on the photocatalytic activity of FMNs1.25, including the initial pH of the wastewater and the catalyst dosage, were determined. The common chemical oxygen demand (CODCr) reduction rate in the case of this sample reached 56.58% within 120 min at a pH of 3, the CODCr of effluent after treatment was 52.10 mg/L. Further, even under neutral conditions, the CODCr of the treated effluent was below the current limit for discharge in China. Moreover, the nanocomposites exhibited good recyclability, and their catalytic activity did not decrease significantly even after five usage cycles. This study should serve as a platform for the fabrication of effective photocatalysts for the advanced treatment of biotreated papermaking effluent and refractory organic wastewater