Magnetic nanoparticles (MNPs) have proven themselves to be useful in biomedical research; however, previous reports were insufficient to address the potential dangers of nanoparticles. Here, we investigated gene expression and metabolic changes based on the microarray and gas chromatography-mass spectrometry with human embryo kidney 293 cells treated with MNPs@SiO(2)(RITC), a silica-coated MNP containing Rhodamine B isothiocyanate (RITC). In addition, measurement of reactive oxygen species (ROS) and ATP analysis were performed to evaluate the effect of MNPs@SiO(2)(RITC) on mitochondrial function. Compared to the nontreated control, glutamic acid was increased by more than 2.0-fold, and expression of genes related to the glutamic acid metabolic pathway was also disturbed in 1.0 μg/μL of MNPs@SiO(2)(RITC)-treated cells. Furthermore, increases in ROS concentration and mitochondrial damage were observed in this MNPs@SiO(2)(RITC) concentration. The organic acids related to the Krebs cycle were also disturbed, and the capacity of ATP synthesis was decreased in cell treated with an overdose of MNPs@SiO(2)(RITC). Collectively, these results suggest that overdose (1.0 μg/μL) of MNPs caused transcriptomic and metabolic disturbance. In addition, we suggest that a combination of gene expression and metabolic profiles will provide more detailed and sensitive toxicological evaluation for nanoparticles.