Tomato fruit are susceptible to postharvest chilling injury when stored at low temperature, thus result in quality deterioration and economic losses worldwide. Protein phosphorylation is an important post-translational modification, which is proven to be involved in plant cold tolerance. But the protein phosphorylation underlying cold stress responses in tomato fruit are remains poorly understood. In this study, we perform comparative phosphoproteomics and provide an overall phosphoprotein profiles in tomato fruit after postharvest cold storage and subsequent shelf-life. A total of 10260 phosphopeptides corresponding to 9640 phosphosites in 3740 phosphoproteins were identified.