Introduction:Recent advancements in androgenetic alopecia (AGA) treatment have highlighted the efficacy of botulinum toxin (BoNT). However, inconsistencies in injection sites and depths warrant attention. It remains unclear which injection strategy is most beneficial for patients. Methods: This split-scalp randomized controlled trial divided each enrolled participant's scalp along the midline: one side was randomized to receive intramuscular BoNT injections in the surrounding muscles, while the other side received intradermal BoNT injections directly into the balding areas. This study evaluated the impact of treatment on hair density and diameter through trichoscopic examinations conducted at baseline and 12 weeks post treatment. Additionally, assessments of pain and overall safety were integrated into the study protocol. Results: Twenty-nine patients completed the study, with significant improvements in hair density observed in the intramuscular injection group compared to the intradermal group (p < 0.001). Both groups exhibited increases in hair diameter, but no significant difference was found between the two methods (p = 0.433). Pain evaluation revealed that intradermal injections in balding areas were more painful than intramuscular injections (p = 0.036), with no severe adverse reactions reported except for a single case of alopecia areata following injection. Conclusion: Our research revealed that both BoNT injection strategies enhanced hair diameter 12 weeks post-treatment, with intramuscular injections significantly improving hair density more effectively. Despite the promising outcomes, the variability in patient responses underscores the necessity for personalized approaches and further research to refine injection protocols for optimized efficacy and safety. Trial Registration Number: ChiCTR2400080190.