Background: Fabry disease (FD) with life-threatening complications occurs as a result of organ damage in kidneys, heart, and brain. Only a few studies, especially from Asia, report their long-term outcome. Methods: In this monocentric study, patients with Fabry nephropathy confirmed by renal biopsy were clinically investigated in a comprehensive manner. The clinic-pathological features, progression, and risk factors for the outcome were analyzed. Results: Thirty-one patients were recruited, after median 62 months (range 8–156 months) follow-up, 23 of them had stable renal function while 8 underwent renal function deterioration. Frequent presenting symptoms included acroparesthesia (58.1%), edema (51.6%), hypo- or anhidrosis (38.7%), and angiokeratoma (32.3%). Left ventricular hypertrophy was present in 62.5% patients with renal function deterioration and 17.4% patients with stable renal function (p = 0.03). The renal cumulative survival rate of all patients was 64.5% in 10 years. Mainz Severity Score Index (MSSI) and segmental sclerosis are independent predictive factors for a more rapid progression of Fabry nephropathy. The receiver operating characteristic analysis demonstrated that the area under the curve for the prediction of renal function progression on the basis of MSSI and segmental sclerosis levels in patients with FD was 0.845 and 0.780, respectively. MSSI score ≥18 or segmental sclerosis ≥3.9% in patients with FD positively correlated with poor renal prognosis. Conclusions: FD’s clinical manifestations are heterogeneous and nonspecific. The 10-year cumulative renal survival rate was low in Chinese patients. MSSI score and segmental sclerosis levels predict the renal prognosis of patients with FD sensitively.