Chronic kidney disease (CKD) is a progressive disease with high morbidity and mortality. Disturbed gut microbiota and toxin accumulation are the main pathologic features of CKD. Current treatments are limited to those that alleviate renal impairment in CKD patients, but few interventions are available that specifically target the regulatory mechanisms of gut microbiota. In this context, researchers urgently need new approaches that can significantly improve survival time and quality of life in these patients. In this review, we outline the involvement of the gut-kidney axis in kidney injury through disturbances of gut microbiota and dysregulation of endogenous metabolites, as well as the prominent contribution of gut microbiota in the discovery of CKD that can be used to prevent, diagnose, and treat CKD. Next, we describe several major metabolites associated with the host-gut microbiota that arise from the synthesis of microbial nutrient transformations and subsequent interactions with the kidney. Then, we summarize the role and potential targets of a compromised gut barrier in CKD. Finally, we discuss research advances in the prevention and treatments of CKD through probiotics modulation of gut microbiota structure to reduce enterogenous toxins and their maintenance of gut barrier function. A growing body of research suggests that intervention through probiotics may be a new and promising therapeutic strategy for CKD.