[Objective] Based on the phosphoproteomics, the expression patterns of proteins phosphorylated were analyzed in tetraploid Citrus wilsonii leaves under drought stress to reveal its response mechanism at the molecular level. [Methods] Phosphorylated proteins in the leaves of tetraploid Citrus wilsonii after drought stress were identified and analyzed using IMAC affinity enrichment and TMT labeling technology. Functional annotation and metabolic pathway analysis of differentially expressed proteins with phosphorylated were also performed. [Results] (1) A total of 3 794 phosphorylation sites and 1 521 phosphorylated proteins were quantified. There were 662 phosphorylated proteins with a fold change exceeding 1.3(αFC>1.3), which mainly located in the nucleus (46.07%) and chloroplasts (24.62%). (2) The differentially expressed proteins with phosphorylated mainly played roles by binding RNA and Ca2+ and participated in metabolic pathways such as RNA splicing, photosynthesis, SNARE interaction in vesicle transport. (3) RT-qPCR results showed that 92.86% genes of differentially expressed proteins with phosphorylated had a consistent trend of change in transcriptional and protein levels and the pearson correlation coefficient was 0.893. [Conclusion] Tetraploid Citrus wilsonii regulated the proteins involved in RNA splicing and photosynthesis pathways through phosphorylation to respond to the drought stress.