Fullerene nanomaterials exposure often causes a variety of diseases. Many studies have pointed out that fullerene nanomaterials can be studied in fish. However, there are few studies on health risk assessment of clownfish with lower doses of fullerene nanoparticles or different exposure durations. In this study, we set 1.5% and 3.0% for low- and high-dose fullerene nanomaterials exposure concentrations, respectively. Meanwhile, we performed a time-series analysis to investigate that the activation of lipid and amino acids metabolism after fullerene nanomaterials exposure in clownfish. 1368 metabolites were detected from clownfish by using liquid chromatography-mass spectrometry (LC-MS) analyses. Our results suggest that exposure to lower fullerenes nanoparticles may have a certain promoting effect on clownfish overall length, body length and weight. At the same time, the activation of potential metabolic pathways enriched by different metabolites in KEGG pathway may also indicate the positive promoting effect of fullerene nanoparticles after exposure. The present work indicates that it is particularly important to find the concentration window for fullerene nanomaterials to improve government safety guidelines, especially when these are applied to assess the health risk of human.