Membranous nephropathy (MN) is one of the leading causes of nephrotic syndrome in adults. However, the current treatment of MN has been a matter of fierce debate for decades, and the needs for more advanced pharmaceuticals are critical for improving the treatment strategies. Sanqi oral solution (SQ), mainly consisting of Radix Astragali and Radix Notoginseng, is a formulated product to treat chronic kidney disease for over 20 years with good efficiency in clinic, while the role of SQ on MN remains unclear. In this study, by establishing an experimental rat model of membranous nephropathy induced by cationic Bovine Serum Albumin (C-BSA), we tried to investigate the effects of SQ. We found that administration of SQ ameliorated MN by reducing proteinuria, elevating serum albumin, and ameliorating pathological renal damages. SQ also significantly reduced the C3 and IgG depositions, and restored podocin and synaptopodin expressions. Furthermore, SQ inhibited the activation of nuclear factor-kappa B (NF-κB) signaling pathway. Our results provide evidence that SQ exerts a novel therapeutic effect on MN via reducing proteinuria, ameliorating renal damage and restoring podocyte injuries, which are associated with the suppression of NFκB.