Fibrosis is a progressive, often irreversible histologic manifestation of chronic and end-stage renal disease. In this study, single-cell transcriptome sequencing technology was used to sequence and analyze blood and kidney tissue cells in normal control rats and rats with chronic kidney disease (CKD), focusing on key cell populations and functional enrichment to explore the pathogenesis of CKD. Oil red O staining and ELISA were used to detect lipid droplets and free fat acid (FFA). RT-PCR, WB were used to verify the differential gene HAO2 and fatty acid metabolic process in tissue to ensure the reliability of single-cell sequencing results. We successfully established a single-cell transcriptome atlas of blood and kidney tissue in rats with CKD, which were annotated into 14 cell subsets (MPCs, PT, Tc, DCT, B-IC, A-IC, CNT, ALOH, BC, Neu, Endo, Pla, NKT, Baso) according to marker gene, and the integrated single-cell atlas of rats showed a significant increase and decrease of MPCs and PTs in the model group, respectively. Functional analysis found extensive enrichment of metabolic-related pathways in PT cells, includes fatty acid metabolic process, cellular amino acid metabolic process and generation of precursor metabolites and energy. Immunohistochemical experiments determined that the differential gene HAO2 was localized in the renal tubules, and its expression was significantly reduced in model group compared with control, and oil red O staining showed that lipid droplets increased in the model group. ELISA assay showed that ATP content decreased in the model group and FFA increased in the model group. ACOX1, PPARα, PGC1α were decreased in the model group, while genes and proteins were increased after overexpression of HAO2, and the AMPK and ACC phosphorylated proteins were increased. Therefore, HAO2 may be an important regulator of fatty acid metabolic processes in CKD, and overexpression of HAO2 can enhance fatty acid metabolism by promoting fatty acid oxidation pathway.