Objective To compare the clinical efficacy of percutaneous neprolithotomy (PCNL) and flexible ureteroscopy (FURS) in the treatment of 2.0-4.5 cm stones in a solitary kidney.Methods We retrospectively analyzed 80 cases of calculi in solitary kidney from August 2012 to May 2018, the sizes of the stones were 2.0-4.5 cm, 43 patients underwent PCNL and 37 patients underwent FURS. The patients'characteristics, stone features, operative time, postoperative hospital stay, hospitalization cost, incidence complications, stone-free rate and renal functions have been evaluated. Results The clinical characteristic of the two groups were comparable.The operative time of PCNL group (103±36) min was shorter than that of FURS group (120±31)min (P=0.039).The postoperative hospitalization stay of PCNL group (9.7±5.1) d was longer than that of FURS group (2.3±1.2) d (P<0.001).The average hospitalization expenses of the PCNL group (29796±10054)yuan were higher than that of the FURS group (19320±7546)yuan (P<0.001).The mean postoperative hemoglobin level of PCNL group (9.3±14.6) g /L was higher than that of FURS group (3.3±3.6)g /L (P=0.014). The postoperative blood transfusion rate of PCNL group was higher than that of FURS(P=0.010).There were 14 cases (32.5%) in the PCNL group using hemostatics after surgery, whereas there was nobody use hemostatics in FURS group, which was statistically significant(P<0.001). Eleven patients (25.6%) and 2 patients (5.4%) of postoperative were treated with pain reliever(P=0.015).There were 7 patients have fever in PCNL group and 4 cases in FURS group (P=0.479).There were no cases of urinary sepsis in either group.The rate of one-session stone removal of PCNL group (86%) was higher than that of FURS (68%) (P=0.048), but there was no significant difference between the two groups in total stone removal rate(P=0.524). Both the levels of serum creatine (Scr) and BUN in the PCNL group decreased after surgery, but only the change of BUN level had statistically significant(P=0.006). There was no statistically significant in the FURS group(P>0.05). Conclusions Both percutaneous nephrolithotomy and flexible ureteroscopy are effective methods for 2.0-4.5 cm stones in a solitary kidney, PCNL has a higher rate of the stone-free rate than FURS, but FURS has less complications, and shorter postoperative hospital stay.