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With the dramatic increment of complexity, more microfluidic devices require 3D structures, such as multi-depth and -layer channels. The traditional multi-step photolithography is time-consuming and labor-intensive and also requires precise alignment during the fabrication of microfluidic devices. Here, we present an inexpensive, single-step, and rapid fabrication method for multi-depth microfluidic devices using a high-resolution liquid crystal display (LCD) stereolithographic (SLA) three-dimensional (3D) printing system. With the pixel size down to 47.25 μm, the feature resolutions in the horizontal and vertical directions are 150 μm and 50 μm, respectively. The multi-depth molds were successfully printed at the same time and the multi-depth features were transferred properly to the polydimethylsiloxane (PDMS) having multi-depth channels via soft lithography. A flow-focusing droplet generator with a multi-depth channel was fabricated using the presented 3D printing method. Experimental results show that the multi-depth channel could manipulate the morphology and size of droplets, which is desired for many engineering applications. Taken together, LCD SLA 3D printing is an excellent alternative method to the multi-step photolithography for the fabrication of multi-depth microfluidic devices. Taking the advantages of its controllability, cost-effectiveness, and acceptable resolution, LCD SLA 3D printing can have a great potential to fabricate 3D microfluidic devices.