Transcranial ultrasound therapy has become a noninvasive method for treating neurological and psychiatric disorders, and studies have further demonstrated that multitarget transcranial ultrasound therapy is a better solution. At present, multitarget transcranial ultrasound therapy in small animals can only be achieved by the multitransducer or phased array. However, multiple transducers may cause spatial interference, and the phased array system is complicated, expensive, and especially unsuitable for small animals. This study is the first to design and fabricate a miniature acoustic holography lens for multitarget transcranial ultrasound therapy in rats. The acoustic holographic lens, working at a frequency of 1.0 MHz, with a size of 10.08 mm ×10.08 mm and a pixel resolution of 0.72 mm, was designed, optimized, and fabricated. The dual-focus transcranial ultrasound generated based on the lens was measured; the full-width at half-maximum (FWHM) of the focal spots in the y -direction was 2.15 and 2.27 mm and in the z -direction was 2.3 and 2.36 mm. The focal length was 5.4 mm, and the distance between the two focuses was 5.6 mm, close to the desired values of 5.4 and 6.0 mm. Finally, the multiple-target blood-brain barrier opening in rats' bilateral secondary visual cortex (mediolateral area, V2ML) was demonstrated using the transcranial ultrasound therapy system based on the lens. These results demonstrate the good performance of the multitarget transcranial ultrasound therapy system for small animals, including high spatial resolution, small size, and low cost.