In the surface environments, magnetite (Fe₃O₄) serves as an electron receptor and donor for microbial extracellular respiration, facilitating interspecies electron transfer as a means to promote the biodegradation of organic pollutants. It has gradually found application in the realm of water pollution remediation. The interplay between magnetite and the mineral-microbe interface assumes a profoundly pivotal role. However, the biodegradation mechanism of PAHs in sediments mediated by different morphologies of magnetite remains unclear. In this paper, two different morphologies of magnetite (micron Fe₃O₄ and nano Fe₃O₄) were prepared to investigate the effect of the magnetite on the biodegradation of PAHs in sediments. Under aerobic conditions, the addition of magnetite did not appreciably reduce the total content of PAHs and certain high-ring PAHs in the sediment. Nevertheless, the introduction of magnetite significantly diminished the levels of low-ring PAHs (naphthalene and phenanthrene) in the sediment. To further investigate the anaerobic biodegradation influence of magnetite on PAHs under varying redox conditions, with phenanthrene as the target pollutant, enrichment and cultivation experiments were conducted with the indigenous degrading microbial communities in the sediment. Two forms of magnetite were introduced under different redox conditions. The results revealed that the augmented treatment with magnetite or electron acceptors somewhat promoted anaerobic biodegradation. Under natural attenuation conditions, the independent addition of micron Fe₃O₄ significantly enhanced phenanthrene degradation, whereas the effect of nano Fe₃O₄ on phenanthrene degradation was more pronounced under sulfate and nitrate reducing conditions. The phenanthrene degradation rate constant under sulfate reducing condition was 1.39 times higher than that of the control treatment. Electron transfer system (ETS) activity demonstrated that the addition of Fe₃O₄ significantly enhances microbial respiration activity.Compared with the control, the ETS activity of the nano-Fe₃O₄ and the micro-Fe₃O₄ treatment increased by 441.7%~511.2% and 113.8%~141.1%, respectively. The microbial community structure indicated that the addition of Fe₃O₄ increased the abundance of aromatic compound-degrading bacteria such as Hydrogenophaga and Ignavibacterium, and relative to micron Fe₃O₄, nano Fe₃O₄ augments the abundance of PAH-degrading bacteria, Achromobacter and Ensifer. Furthermore, nano Fe₃O₄ may mediate intermicrobial electron transfer by releasing more Fe(II) and Fe(III). These findings contribute to a deeper comprehension of the pivotal role of magnetite in the biodegradation of organic pollutants, offering a potential approach for the remediation of contaminated sediments.