Naphthalene has remained a challenge how to eradicate it from the water because of its carcinogenic risk to humans. In the present study, naphthalene prominently increased the rates of embryonic mortality and malformation, and decreased the hatchability of zebrafish which have a high developmental similarity to humans. Moreover, multiple-organ toxicity were notably found in naphthalene-treated zebrafish. Here, irradiated graphene aerogel (IGA) was successfully prepared from high-energy electron beam to generate more wrinkles, folds, defects and a strong absorption capability for naphthalene, compared with the non-irradiated graphene aerogel. IGA was outstandingly found to remove naphthalene from the embryo culture medium, and subsequently inhibit the embryotoxicity and maintain tissue integrity by restoring cardiac function, attenuating apoptosis signals, recovering eye morphology and structure, reducing expression of heat shock protein 70 in the tissues and promoting behavioral capacity. Meanwhile, no obvious negative impact of IGA was found in the developing zebrafish from embryo to larvae. Consequently, reduction in the toxicity of naphthalene during zebrafish embryogenesis was mediated by IGA as an advanced strategy.