Objective To evaluate the effect of brain-derived neurotrophic factor (BDNF) gene polymorphism on the recovery period of dexmedetomidine during laparoscopic hysterectomy anesthesia.Methods A total of 98 patients underwent laparoscopic hysterectomy from August to January 2019 in our hospital were included. All patients received dexmedetomidine. The expression of rs6265 in BDNF gene was determined by PCR-RFLP, and the patients were divided into GG Group, GA Group, and AA group, according to genotype. The basic characteristics, visual analogue scale (Vas) score, comfort scale (BCS-RRB) score, quality of resuscitation, and side effects were compared in patients with different genotypes.Results The genotype frequency of rs6265 site of BDNF gene was in accordance with Hardy-weinberg equilibrium (P > 0.05) , and there was no significant difference in age, body mass index (BMI), American Society of anesthesiologists (ASA), disease type, operation time, and intraoperative bleeding among 3 groups (P > 0.05). Comparison of VAS and BCS scores in the 3 groups at 4 h, 12 h, and 24 h after surgery, with repeated measures design analysis of variance, showed differences at different time points (P < 0.05). The VAS score and BCS score of the 3 groups were different (P < 0.05). Compared with the GG group and the GA group, the AA group had a higher VAS score and a lower BCS score, and the relative analgesia effect and comfort were worse. The VAS scores and BCS score change trend of the 3 groups were significantly different (P < 0.05). Wake time, spontaneous breathing recovery time, and extubation time were longest in group AA, followed by group GA and group GG, respectively (P < 0.05). The incidence of adverse reactions in AA group (41.38%) was significantly higher than that in GG group (17.86%) and GA group (14.63%) (P < 0.05).Conclusion The rs6265 locus polymorphism of the BDNF gene is closely related to the anesthesia effect of dexmedetomidine used in laparoscopic hysterectomy. The genotype carrying the A allele (AA+AG) may prolong the recovery time, increase the degree of pain and adverse effects, reduce comfort, and affect postoperative cognitive function.