Objective To investigate the application of endoscopic ultrasound-guided liver biopsy (EUS-LB) to liver transplant recipients. Methods In this retrospective cohort study, a total of 12 liver transplant recipients who underwent EUS-LB by the same endoscopist and specimens were diagnosed and reported by the same pathologist due to abnormal liver function or need to be evaluated for graft fibrosis in the Organ Transplantation Center of the Affiliated Hospital of Qingdao University were enrolled into the EUS-LB group from December 2021 to March 2022, meanwhile, a total of 23 patients whose PLB was completed by the same hepatologist and specimens were diagnosed by the same pathologist during the same period were enrolled in the PLB group. Acquisition of liver specimens and postoperative adverse events of the two groups were compared. Results Patients in both groups were punctured 1-2 times on average, and the median total length of liver specimens in the EUS-LB group was significantly longer than that in the PLB group (61 mm VS 17 mm, Z=11.362, P=0.002). There was no significant difference in the length of the longest liver specimens between the two groups (17.6±6.9 mm VS 13.7±3.5 mm, t=2.382, P=0.086), while the number of liver specimens in the EUS-LB group was more than that in the PLB group (4.8±2.1 VS 2.3±1.2, t=9.271, P=0.001). The number of complete portal tracts was 11.3±4.6 in the EUS-LB group and 6.2±3.3 in the PLB group (t=8.457, P=0.003). Abdominal pain was the only postoperative adverse event, and only 1 patient in the EUS-LB group had postoperative abdominal pain, which was fewer than that in the PLB group [8.3% (1/12) VS 43.5% (10/23), χ2=4.893, P=0.036]. Conclusion Compared with PLB, EUS-LB delivers longer liver biopsy specimens with more complete portal tracts in liver transplant recipients, and fewer recipients complain about postoperative pain in EUS-LB group. Therefore, EUS-LB is a safer, more effective and more comfortable liver biopsy method.