Self-assembly of droplets guided by microfluidic channels have potential applications ranging from high throughput assays to materials synthesis, but such demonstrations have been limited primarily to two-dimensional (2D) assembly of droplets in planar microfluidic devices. We demonstrated the use of three-dimensional (3D) microchannels to self-assemble droplets into ordered 2D and 3D arrays by designing microchannels with axial gradients in height and controlling the volume fraction of the droplets in the channel. In contrast to previous demonstrations, ordered 2D arrays of droplets were assembled at low volume fractions of the dispersed phase. Interestingly, we found that the self-assembly of droplets in microchannels was highly path dependent. The assembly of droplets was governed by transitions in the cross-sectional shapes of the microchannel, not the final geometry of the chamber for the assembly of droplet, which is a hitherto rarely explored phenomenon. The assembled droplets were used as templates for the fabrication of millimeter scale, anisotropic hydrogel fibers with ordered pore sizes (∼250 μm). These demonstrations suggested that 3D microchannels would be a viable platform for the manipulation of droplets, and applicable for the continuous synthesis of complex materials with 3D morphologies.