While vat photopolymerization has many advantages over soft lithography in fabricating microfluidic devices, including efficiency and shape complexity, it has difficulty achieving well-controlled micrometer-sized (smaller than 100 μm) channels in the layer building direction. The considerable light penetration depth of transparent resin leads to over-curing that inevitably cures the residual resin inside flow channels, causing clogs. In this paper, a 3D printing process — in-situ transfer vat photopolymerization is reported to solve this critical over-curing issue in fabricating microfluidic devices. We demonstrate microchannels with high Z-resolution (within 10 μm level) and high accuracy (within 2 μm level) using a general method with no requirements on liquid resins such as reduced transparency nor leads to a reduced fabrication speed. Compared with all other vat photopolymerization-based techniques specialized for microfluidic channel fabrication, our universal approach is compatible with commonly used 405 nm light sources and commercial photocurable resins. The process has been verified by multifunctional devices, including 3D serpentine microfluidic channels, microfluidic valves, and particle sorting devices. This work solves a critical barrier in 3D printing microfluidic channels using the high-speed vat photopolymerization process and broadens the material options. It also significantly advances vat photopolymerization’s use in applications requiring small gaps with high accuracy in the Z-direction.