Studies on the relationship between body mass index (BMI) and renal progression in IgA Nephropathy (IgAN) were limited, especially for underweight patients with IgAN. To elucidate the clinical features and effect of underweight on renal function deterioration in this disease, we recruited IgAN patients with diagnostic age ≥18 years old and a baseline estimated glomerular filtration rate (eGFR) ≥15 ml/min/1.73m2 from our center between 1985 and 2014. Patients secondary to systemic diseases or follow-up less than 6 months were excluded. All patients' clinical data at renal biopsy and during follow-up were recorded. Renal outcome was defined as end-stage kidney disease (ESRD). Baseline body mass index (BMI) was calculated by weight (kg) over squared height (m2). According to WHO Asian guideline, BMI was categorized as follows: <18.5kg/m2 (underweight), 18.5-22.99kg/m2 (normal weight), 23-27.49kg/m2 (overweight) and obese (≥27.5 kg/m2). Of 930 primary IgAN patients enrolled in this study, mean age at renal biopsy was 37.6 years and 49.2% were men. Totally, 114 (12.3%) ESRD occurred after a mean follow-up of 47.1 months. More ESRD happened in underweight patients (17.3%) compared to patients with normal weight (13.2%), overweight (11.0%) or obesity (9.5%). By multivariate Cox regression analysis, underweight was independently associated with a higher risk of ESRD after adjustment for demographic characteristics and clinical variables (HR: 3.5, 95% CI: 1.3-9.5, P = 0.01) comparing to normal weight. Underweight patients had lower hemoglobin, serum uric acid, triglycerides, cholesterol and lymphocyte counts than patients with normal weight. Furthermore, BMI was positively correlated with serum C3 (r = 0.25, p <0.001). Our research finds that underweight is an independent risk factor for kidney disease progression in IgAN, which might be associated with malnutrition status and decreased C3 levels.