Background <p>The incidence rate of idiopathic membranous nephropathy (IMN) has been increasing, and its pathogenesis is still unclear. Exploring new diagnostic molecular markers and the molecular mechanisms of IMN.</p> Methods <p>Fifteen healthy controls and fifteen IMN patients were recruited. Clinical baseline data of all participants, including age, gender, and body mass index (BMI), along with histopathological staging (Ehrenreich-Churg classification) and immunohistochemical staining results for phospholipase A2 receptor (PLA2R), were collected and analyzed. Meanwhile, peripheral blood and urine samples were obtained to detect renal function-related biochemical indicators, including serum creatinine (Scr), estimated glomerular filtration rate (eGFR), serum albumin, 24-hour urinary protein (24&#xa0;h UPT), serum total cholesterol (TC), anti-PLA2R antibody titer, and serum immunoglobulin G (IgG). Urine samples (<i>n</i> = 10) were also used for high-throughput sequencing analysis.</p> Results <p>Serum albumin was significantly downregulated in the IMN group, while 24&#xa0;h UPT, TC, anti-PLA2R Ab titer, and IgG were upregulated. MicroRNA (miRNA) transcriptomic analysis identified 34 differentially expressed (DE) miRNAs. Hsa-miR-576-3p, hsa-miR-766-5p, and NovelmiRNA-837 exhibited strong diagnostic potential via ROC curve analysis (AUC &gt; 0.8). Sixty-four DE mRNAs were identified in IMN tissues, with enrichment in pathways such as Ribosome and MAPK signaling-fly. ENST00000481739 (RXRA) was upregulated in IMN, correlated with anti-PLA2R Ab titer, and exhibited diagnostic potential (AUC = 0.929). Thirty-five DE lncRNAs were identified in IMN, enriched in autophagy, mitophagy, and apoptosis pathways. TCONS_00180924, TCONS_00176280, TCONS_00208611 correlated significantly with TC, 24-h urinary protein, and anti-PLA2R Ab titer.</p> Conclusions <p>This study provides a foundation for developing non-invasive diagnostic tools and targeted therapies for IMN.</p>