In the present study, quantitative analysis coupled with toxic evaluation was applied to investigate the influence of sulfur-fumigation on the quality of Chrysanthemum morifolium. The results showed that the average contents of six flavonoids (cynaroside, hyperoside, isoquercitrin, luteolin, apigenin, and diosmetin) in sulfur-fumigated C. morifolium samples decreased by about 6.2%, 3.5%, 22.0%, 33.3%, 26.0%, and 36.9%, respectively, while the average contents of two organic acids (chlorogenic acid and isochlorogenic acid A) in sulfur-fumigated C. morifolium samples increased by about 16.8% and 7.6%, respectively. Furthermore, high dosage sulfur-fumigated C. morifolium could induce hydropic degeneration in epithelial cells of the renal tubule and interstitial edema. This indicates that sulfur-fumigated C. morifolium may lead to renal toxicity.