Protein phosphorylation, especially serine/threonine and tyrosine phosphorylation, plays significant roles in signaling processes during plant growth and development as well as their responses to biotic or abiotic stresses. The dual-specificity protein tyrosine phosphatases are important to de-phosphorylate and inactivate the signaling components. In this study, we reported an atypical dual specificity protein tyrosine phosphatase ATPFA-DSP3 (DSP3), which loss-of-function mutant was insensitive to salt treatment, played a negative role in plant’s response to salinity in Arabidopsis. DSP3 protein was primarily localized in nuclei and degraded after salt treatment. The level of ROS accumulation was lower in dsp3 mutant and higher in DSP3 over-expresser than wild type control, indicating DSP3 positively affect ROS production. DSP3 can directly interact with MPK3 and MPK6, and the phosphorylated MPK3 and MPK6 over accumulate in dsp3 mutant. Moreover, the phosphatase activity of DSP3 was required for its salt response. These results provide evidences showing that DSP3 negatively mediates plant salt response by directly modulating the accumulation of phosphorylated MPK3 and MPK6.