Manganese (Mn) is an essential trace element, but excessive exposure can damage mental, cognitive, and motor functions. Although many studies have reported the toxicity of Mn, the underlying mechanism remains unclear. Here, wild-type and/or Tg(NBT:DsRed) zebrafish embryos/larvae were exposed to different dosages of Mn to determine the effects on mortality, malformation, and hatching rates. A video tracking system was used to analyze the locomotor activities of zebrafish larvae. The terminal deoxynucleotidyl transferase dUTP nick end labeling assay and acridine orange staining were performed to monitor cell apoptosis, while dopamine transporter and tyrosine hydroxylase (TH) expression were detected by immunohistochemical staining. Meanwhile, transcriptome sequencing of the head tissues of zebrafish larvae was performed to search for molecular targets of Mn neurotoxicity. The results showed that Mn exposure increased the mortality and malformation rates of zebrafish larvae, and significantly reduced swim distance and velocity. In addition, the proportion of apoptotic dopaminergic neurons increased, while TH expression significantly decreased. The results of transcriptome sequencing showed that a large number of differentially expressed genes associated with apoptosis and DNA damage repair were upregulated, consistent with the above results. Meanwhile, Western blot analysis showed that higher exposure level of Mn could induce activation of MAPK pathway. These data demonstrate that Mn exposure can damage dopaminergic neurons and cause apoptosis, which has detrimental effects on the motor abilities of zebrafish larvae.