Objective To analyze the application effect of microneedle fractional radiofrequency in facial rejuvenation. Methods A total of 70 patients who received facial rejuvenation treatment in Baoying County Dermatology Prevention and Treatment Hospital from January to December 2025 were selected as the research subjects. According to the random number table method, they were divided into the control group and the observation group, with 35 patients in each group. The control group was treated with botulinum toxin type A, and the observation group was treated with microneedle fractional radiofrequency. The excellent and good rate of facial rejuvenation, improvement of facial skin quality, facial skin status and adverse reaction rate were compared between the two groups. Results The excellent and good rate of facial rejuvenation in the observation group (97.14%) was higher than that in the control group (77.14%) (P <0.05). All indicators of facial skin quality improvement in the observation group after treatment were better than those in the control group (P <0.05). After treatment, the stratum corneum hydration in the observation group was better than that in the control group, and the average fine line depth of the whole face was lower than that in the control group (P <0.05). There was no statistically significant difference in the incidence of adverse reactions between the two groups (P >0.05). Conclusion Microneedle fractional radiofrequency can effectively reduce the depth of facial fine lines, increase stratum corneum hydration, improve sebum secretion, dark pigmentation and skin elasticity, and achieve favorable overall efficacy for facial rejuvenation, with good safety.