Epilepsy is the fourth most common neurological disorder, and aberrantly elevated sulfur dioxide derivatives (SO32−/HSO3−) are thought to underlie the hippocampal neuronal apoptosis in epilepsy. We have designed and synthesized a mitochondria-targeted polydopamine nanoprobe for visualizing endogenous SO32−/HSO3− by the nucleophilic addition reaction. The nanoprobe was used for imaging SO2 derivatives both in the mitochondria of cultured cells and zebrafish, and successfully applied in the hippocampus of a rat model of epilepsy. The PDAD nanoprobe could be of great value for the elucidation of mechanisms of abnormal SO32−/HSO3− involved in diseases such as epilepsy.