Hematopoietic stem cell transplantation (HSCT) is a standard form of cellular therapy for patients suffering from malignant hematological diseases. However, graft-versus-host disease (GVHD) is a very serious complication and a major cause of morbidity and mortality after allogeneic HSCT. Calcineurin inhibitors, such as cyclosporine, are widely used to enhance the survival of patients who have undergone HSCT. Unfortunately, both GVHD and cyclosporine occasionally cause nephropathy. Several studies have shown that the gut-kidney axis is associated with nephropathy. Dysbiosis of the gut microbiota might aggravate renal damage by increasing systemic micro-inflammation, suggesting that diet might affect the risk of GVHD. Here, we summarized the recent findings regarding the association between the alteration of gut microbiota and nephrotoxicity. The results suggested that treatment with certain probiotics benefits the symbiosis in the gut-kidney axis and makes HSCT safer.