Hepatocellular carcinoma (HCC) is the most common malignancy of the liver, posing a significant threat to public health. Although liver transplantation (LT) is an effective treatment for HCC, ischemia-reperfusion (I/R) injury, transplant rejection, and complications after LT can greatly reduce its effectiveness. In recent years, transplant oncology has come into being, a comprehensive discipline formed by the intersection and integration of surgery, oncology, immunology, and other related disciplines. Gut microbiota, an emerging field of research, also plays a crucial role. Through the microbiome-gut-liver axis, the gut microbiota has an impact on the onset and progression of HCC as well as LT. This review summarizes the mechanisms by which the gut microbiota affects HCC and its bidirectional interactions with chronic liver disease that can develop into HCC as well as the diagnostic and prognostic value of the gut microbiota in HCC. In addition, gut microbiota alterations after LT were reviewed, and the relationship between the gut microbiota and liver I/R injury, the efficacy of immunosuppressive drugs used, and complications after LT were discussed. In the era of LT oncology, the role of the gut microbiota in HCC and LT should be emphasized, which can provide new insights into the management of HCC and LT via gut microbiota modulation.