Objectives: Coronavirus Disease 2019 (COVID-19) not only causes lung damage but also induces renal damage, but the molecular mechanism remains unclear. Methods: Six rhesus macaques were divided into a control group and a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection group. Meanwhile, their kidneys were segmented into three regions: renal cortex (Cor), inner medulla (IM), and outer medulla (OM), and liquid chromatography-tandem mass spectrometry-based proteomics and phosphoproteomic analysis were conducted. Next, we performed a comprehensive bioinformatics analysis, including differential analysis, functional enrichment, kinase prediction and drug target prediction in order to identify key molecules associated with COVID-19. Results: We established proteomic and phosphoproteomic profiles of Cor, OM and IM of rhesus macaque kidneys infected with SARS-CoV-2. Renal injury was observed in three regions, implicating various organelles and biological processes such as ribosomes, spliceosomes, glycolysis/gluconeogenesis, IL-17 signaling pathway and Toll-like receptor signaling pathway. Additionally, varying intensities of inflammatory reactions, metabolic perturbations and fibrosis were evident in all regions. By utilizing DrugBank, we identified 21 FDA-approved drugs targeting predicted kinases as candidates for treatment. Minocycline, acetylcysteine, and fostamatinib have been used to treat COVID-19-associated kidney injury. Conclusions: This study provides a comprehensive dataset and atlas of proteomics and phosphoproteomics of SARS-CoV-2 infected rhesus macaque kidneys.