The objective was to explore the relative indications of free vascularized fibular graft (FVFG) and Ilizarov bone transport (IBT) in the treatment of infected bone defects of lower extremities via comparative analysis on the clinical characteristics and efficacies. The clinical data of 66 cases with post-traumatic infected bone defects of the lower extremities who underwent FVFG (n = 23) or IBT (n = 43) from July 2014 to June 2018 were retrieved and retrospectively analyzed. Clinical characteristics, operation time, and intraoperative blood loss were statistically compared between two groups. Specifically, the clinical efficacies of two methods were statistically evaluated according to the external fixation time/index, recurrence rate of deep infection, incidence of complications, the times of reoperation, and final functional score of the affected extremities. Gender, age, cause of injury, Gustilo grade of initial injury, proportion of complicated injuries in other parts of the affected extremities, and numbers of femoral/tibial defect cases did not differ significantly between treatment groups, while infection site distribution after debridement (shaft/metaphysis) differed moderately, with metaphysis infection little more frequent in the FVFG group (P = 0.068). Femoral/tibial defect length was longer in the FVFG group (9.96 ± 2.27 vs. 8.74 ± 2.52 cm, P = 0.014). More patients in the FVFG group presented with moderate or complex wounds with soft-tissue defects. FVFG treatment required a longer surgical time (6.60 ± 1.34 vs. 3.12 ± 0.99 h) and resulted in greater intraoperative blood loss (873.91 ± 183.94 vs. 386.08 ± 131.98 ml; both P < 0.05) than the IBT group, while average follow-up time, recurrence rate of postoperative osteomyelitis, degree of bony union, and final functional scores did not differ between treatment groups. However, FVFG required a shorter external fixation time (7.04 ± 1.72 vs. 13.16 ± 2.92 months), yielded a lower external fixation index (0.73 ± 0.28 vs. 1.55 ± 0.28), and resulted in a lower incidence of postoperative complications (0.87 ± 0.76 vs. 2.21±1.78, times/case, P < 0.05). The times of reoperation in the two groups did not differ (0.78 ± 0.60 vs. 0.98 ± 0.99 times/case, P = 0.615). Both FVFG and IBT are effective methods for repairing and reconstructing infected bone defects of the lower extremities, with unique advantages and limitations. Generally, FVFG is recommended for patients with soft tissue defects, bone defects adjacent to joints, large bone defects (particularly monocortical defects), and those who can tolerate microsurgery.