Purpose. To compare the clinical efficacy, safety, and histological effect between ultrasound cycloplasty (UCP) and cyclocryotherapy in the treatment of neovascular glaucoma. Methods. Two groups of neovascular glaucoma patients who underwent two types of treatment, respectively, namely, 26 patients treated by UCP and 23 by cyclocryotherapy, were treated and observed during the clinical study for six months. The primary outcome was evaluated by the surgical success, which was defined as the intraocular pressure (IOP) reduction of greater than or equal to 20% from the baseline and the IOP value of greater than 5 mmHg at the last follow-up. The secondary outcome referred to pain relief, complications, and the mean of the IOP at each follow-up. In the animal experiment, 18 New Zealand rabbits were divided into two groups and treated by UCP and cyclocryotherapy, respectively. The changes in the tissues and in the expression of matrix metalloproteinase-1 (MMP-1) were observed immediately. Results. The mean IOP baseline for the UCP and cyclocryotherapy groups was 54.6 ± 9.7 mmHg and 53.3 ± 11.7 mmHg, respectively. After six months of follow-up, the IOP value decreased to 30.3 ± 9.4 mmHg for the patients treated by UCP and to 30.4 ± 9.1 mmHg for those treated by cyclocryotherapy. The two groups achieved a satisfying success rate in the treatment of neovascular glaucoma of up to 70% at least. Vision impairment was observed in some patients treated with cyclocryotherapy, and these patients suffered from more complications and less pain relief than the patients who were treated with UCP. The histological study showed that the ciliary body was completely destroyed after cyclocryotherapy and that MMP-1 was found only in the ciliary muscle. After the UCP treatment, MMP-1 could still be found in the ciliary body, and only the double-layer epithelial cells presented with coagulative necrosis. Conclusion. The UCP treatment and cyclocryotherapy both showed good efficacy in significantly reducing the IOP. However, the UCP treatment was safer with less postoperative complications and adverse effects. Thus, the overall treatment effect of the UCP was more efficient than that of cyclocryotherapy.