Objectives Free fibula flap is the first choice for jaw reconstruction in head and neck oncology, but postoperative complications in donor site are ignored always. The main purpose of this study was to investigate the long-term complications and potential risk factors of donor site after vascularized fibular transplantation, and to explore the precautions of preparing vascularized fibular flap and the measures of preventing donor site complications. Materials and methods Data were retrospectively collected on 31 patients who had undergone immediate mandibular reconstruction with a fibular flap after segmental mandibulectomy from 2013 to 2018 in Shanghai Ninth People's Hospital. Thirty-one patients (24 male, 7 female) were available for the long-term complications in donor site analysis from 25 to 96 months after surgery. The data were collected and analyzed, including age at time of operation, early postoperative complications, incidence of dorsiflexion weakness of hallux, donor site missing fibula length, proximal and distal stump fibula length, and subjective evaluation of foot function (AOFAS-hallux, AOFAS-ankle hindfoot, Enneking lower limb function score). In the single-factor analysis in this study, the correlation between related factors and long-term complications was statistically analyzed. For inter-group comparisons of quantitative data, if the normal distribution was satisfied, two independent sample t-tests were used; p < 0.05 was statistical significant. If the normal distribution was not satisfied, Wilcoxon rank-sum test was used, and p < 0.05 was considered statistically significant. For qualitative data, the Fisher exact probability method was compared between group differences, and p < 0.05 was statistically significant. Results The most commonly encountered complication in our series was dorsiflexion disorder, flexion deformity, numbness of the lateral side of the lower leg, and dorsum of the foot. Ten patients (32.26%) developed hallux flexion deformity after operation, 17 patients (54.84%) had hallux dorsiflexion dysfunction after operation, and 10 patients (32.26%) had numbness of the lateral side of the lower leg and dorsum of the foot. The incidence of hallux dorsiflexion dysfunction, thumb flexion deformity, and sensory disturbance was higher than that of other long-term complications in the donor area. The residual length of fibular distal was related to the dorsiflexion dysfunction and flexion deformity of hallux (p < 0.05). The early complications of donor site were correlated with the hallux dorsiflexion dysfunction (p < 0.05). Conclusions The incidence of dorsiflexion disorder and flexion deformity is higher in patients after fibula transplantation. The less the residual length of fibular distal, the more obvious the long-term complications in the donor site, and the higher the incidence of dorsiflexion dysfunction and flexion deformity of hallux.