With the major constituent of cell membranes coated on the surface, phosphatidylcholine-coated magnetic nanoparticles (P-MNPs) which have been shown to have low toxicity and good dispersion, are widely used in biomedical applications, such as drug-delivery, magnetic resource imaging and hyperthermia. However, the effects of P-MNPs in vivo with magnetic field exposure have been evaluated poorly. The present study was focused on the interference of lipid metabolism by P-MNPs under 0.5 T static magnetic fields (SMFs) in Caenorhabditis elegans (C. elegans). The P-MNPs were accumulated in the intestine of nematodes, where fatty acids are accumulated. The content of lipofuscin was decreased in C. elegans exposed to either P-MNPs or SMF, while there were no further decrease in worms with P-MNPs+ SMF exposure. However in the presence of SMF, the lipid content was greatly decreased in C. elegans in the P-MNPs+ SMF exposure groups. The constituents of long-chain fatty acids and polyunsaturated fatty acids analyzed by gas chromatography (GC) were significantly decreased in P-MNPs treated worms under 0.5 T SMF, which was consistent with the mRNA expression of fatty acid metabolism genes including elo-2, let-767 and fat-5. Our results indicated that the lipid metabolism interfered by P-MNPs via the accelerated beta oxidation and changed gene expression in C. elegans under 0.5 T SMF.