Diabetic kidney disease (DKD) is a primary cause of end-stage renal disease. Proteinuria is a clinical indicator of the different stages of DKD, and podocyte injury is a major cause of proteinuria. Podocyte-specific proteins (PSPs) play important roles in the normal filtration of podocytes. Studies have shown that natural active compounds (NACs) can ameliorate proteinuria; however, the mechanism related to PSPs needs to be explored. In this study, the five stages of DKD related to proteinuria and the functions of PSPs are displayed separately. Mechanisms for ameliorating proteinuria and improving the PSPs of the 15 NACs are summarized. The
in vitro
and
in vivo
mechanistic research showed that five compounds, astragaloside IV, ligustrazine, berberine, emodin and resveratrol, exerted renal protective effects
via
AMPK signaling, icariin and berberine
via
TLR4 signaling, hirudin and baicalin
via
MAPK signaling, curcumin and baicalin
via
NF-κB signaling, and emodin
via
protein kinase RNA-like endoplasmic reticulum kinase signaling. The 13 PSPs were divided into five categories: actin cytoskeleton, basal domain, apical domain, slit diaphragm, and others. In conclusion, anti-inflammatory effects, anti-oxidative stress, and enhanced autophagy are the main mechanisms underlying the ameliorative effects of NACs. Podocyte apoptosis is mainly related to nephrin and podocin, which are the most studied slit diaphragm PSPs.