Chronic kidney disease (CKD) is a global health problem, and its incidence increases year by year. Studies have revealed that the progression of CKD into end-stage renal disease (ESRD) is related to its inability to effectively eliminate toxins due to decreased renal function. Additionally, intestinal microflora produces a large amount of gut-derived uremic toxins (GDUTs) during protein fermentation. The theory of gut-kidney axis holds that gut and kidney interact with each other, and CKD reduces the ability to remove uremic toxins (UTs), resulting in the accumulation of UTs in the blood. The accumulation of UTs also accelerates the deterioration of renal function, leading to a vicious circle. This paper focused on the sources of indoxyl sulfate and p-cresol sulfate in GDUTs and their mechanisms against CKD (such as inducing renal tubular cell death, oxidative stress and endothelial injury, promoting renal fibrosis and down-regulating renal protective protein) as well as the sources of trimethylamine oxide and its mechanisms against CKD (such as promoting renal fibrosis and inflammation). Moreover, starting from gut-kidney axis, this paper summarized the ways of diet and nutrition regulation, toxin adsorption, enhanced dialysis to increase the clearance, inhibiting the sources of gut-derived toxins and traditional Chinese medicine (TCM) therapy (TCM preparations and TCM active ingredients) to regulate intestinal microecology and reduce the generation of GDUTs, aiming to provide new therapeutic ideas for delaying the progression of CKD.