Mesangial proliferative glomerulonephritis (MsPGN) is the most common glomerulonephritis pathological type, including IgA nephropathy (IgAN), in which regional immune injury leads to disease progression without targeted treatment approaches. The mechanism of regional immune injury in MsPGN is unclear. We previously performed single-cell RNA sequencing (scRNA-seq) of IgAN and identified that the CX3CR1 gene increased in kidney. In this study, further scRNA-seq analysis and cellchat analysis revealed that CX3CL1 and CX3CR1 expression was increased in mesangial cells and monocytes/macrophages, respectively, in IgAN, mediating stronger crosstalk. This result and its association with regional immune injury were validated in clinical specimens and MsPGN animal model. Deficiency of CX3CR1+ monocytes/macrophages in the MsPGN animal model attenuated proteinuria, cell proliferation, and inflammation in glomerulus. Mechanistically, CX3CL1 in activated mesangial cells induced CX3CR1+ monocyte/macrophage migration and activation, and RNA-seq, Luminex multiplex immunoassay, and molecular analysis revealed that CX3CR1+ monocytes/macrophages induced mesangial cell injury via the MIF-CD74 interaction and activated the phosphatidylinositol 3-kinase (PI3K)/proteinserine-threonine kinase (AKT) pathway. Lastly, the therapeutic effect of the CX3CL1 monoclonal antibody quetmolimab was validated for inhibiting the progression of MsPGN. These findings demonstrate that activated mesangial cells interact with CX3CR1+ monocytes/macrophages promoting glomerulus regional immune injury in MsPGN, providing evidence into the CX3CL1-CX3CR1 axis as a novel target of treatment for MsPGN.