Droplet-based single-cell sequencing has emerged as a very powerful tool to study the cellular heterogeneity in diseased tissues for a variety of biological problems. However, the current droplet generation with a single particle and cell encapsulation is a random process and suffers from a low yield that is unable to fulfill the high-throughput analysis requirement. In this work, we present a new fluorescence-activated droplet sorting (FADS) system that can isolate single-cell droplets at high accuracy and high yield using a highly focused surface acoustic wave (HFSAW) with a beam width around 50 μm. The acoustic wave is locally coupled into the microfluidic channel for droplet sorting through a micropillar waveguide structure between the channel and the interdigitated transducer (IDT). This detachable acoustic sorting system allows the disposal of the microfluidic channel after a single use to avoid cross-contamination and keeps the expensive IDT device reusable. We have achieved rapid and accurate isolation of single-cell droplets with purity higher than 90% at ∼1 kHz sorting rate with three different encapsulation contents. In addition, with the uniformly produced droplet size at ∼40 μm, the present acoustic FADS system enables effective sorting of small particles down to submicrometer size, which is challenging for existing fluorescence-activated cell sorting systems.