The current conservative and surgical treatments are not fully effective and have complications for Raynaud's phenomenon (RP) secondary to systemic sclerosis (SSc). Botulinum toxin A (BTX-A) can be used to manage RP, but the literature mostly includes case reports and case series. Thus, we performed a randomized controlled trial to explore the efficacy of BTX-A in the treatment of RP secondary to SSc. Sixteen patients with RP secondary to SSc were recruited. One hand was randomly included in the BTX-A group and the other as control. Both hands were tested before treatment and 4 weeks later using qualitative and quantitative dermatoscopic assessments and the cold water test. Reynolds score (from 6.7 +/- 4.0 to 2.9 +/- 3.7, p < 0.001), T-base (from 25.8 +/- 3.0 degrees C to 27.9 +/- 2.1 degrees C, p = 0.031) and T-change (from 2.1 +/- 1.2 degrees C to 4.5 +/- 2.1 degrees C, p < 0.001) in the experimental group were improved, while there were no improvements in T-base and T-change in the control group. In the experimental group, the sum of the six dermoscopic parameters was improved after treatment (from 4.00 (3.00, 5.75) to 3.00 (2.00, 5.00), p = 0.002); the nailfold capillary pattern staging was also improved (from 2.00 (2.00, 3.00) to 2.00 (1.00, 3.00), p = 0.004). There were no improvements in the dermoscopic assessment in the control group. None of the patients reported adverse reactions such as infection, hematoma, hand muscle weakness, allergic reaction and nerve injury. In conclusion, local injection BTX-A to treat RP secondary to SSc might be safe and effective.