Patients with diabetes mellitus complicated with proteinuria can be diabetic nephropathy (DN), diabetic complicated with non-diabetic kidney disease (NDKD), or DN with NDKD. Among these membranous nephropathy accounted for a large proportion of DN with NDRD. At present, serum anti-phospholipase A2 receptor (PLA2R) antibody is widely used in the diagnosis and evaluation of therapy in idiopathic membranous nephropathy, our study aimed to investigate the diagnostic significance of anti-PLA2R antibody in type 2 diabetes mellitus (T2DM) patients with proteinuria, providing a method for patients with contraindications of kidney biopsy. Eighty-seven T2DM patients with proteinuria who went on kidney biopsy were divided into the DN group, idiopathic membranous nephropathy (IMN) group, and others group according to their pathological results. In our study, 52.87% and 28.74% of patients were found to have IMN and diabetic nephropathy respectively. The levels of anti-PLA2R antibody, total cholesterol, triglyceride, and estimated glomerular filtration rate (eGFR) were higher in the IMN group, while the prevalence of diabetic retinopathy (DR), systolic blood pressure (SBP) and HbA1c were higher in the DN group. For T2DM patients with proteinuria, anti-PLA2R antibody (AUC = 0.904, 95%CI 0.838–0.970) has a high diagnostic value for IMN. The duration of diabetes (OR = 0.798, P = 0.030), eGFR level (OR = 1.030, P = 0.024), and positive anti-PLA2R antibody (OR = 72.727, P < 0.001) favor the diagnosis of IMN, while DR (OR = 50.234, P < 0.001), SBP (OR = 1.041, P = 0.030), and negative anti-PLA2R antibody (OR = 0.008, P = 0.001) is beneficial to the diagnosis of DN. Our study found that NDKD is not uncommon in patients with T2DM and proteinuria, and IMN was the main pathological type. Positive anti-PLA2R antibody has a strong accuracy in the diagnosis of IMN in patients with T2DM and proteinuria.