In this work, we introduce a roll-to-roll system that can continuously print three-dimensional (3D) periodic nanostructures over large areas. This approach is based on Langmuir-Blodgett assembly of colloidal nanospheres, which diffract normal incident light to create a complex intensity pattern for near-field nanolithography. The geometry of the 3D nanostructure is defined by the Talbot effect and can be precisely designed by tuning the ratio of the nanosphere diameter to the exposure wavelength. Using this system, we have demonstrated patterning of 3D photonic crystals with a 500 nm period on a 50 × 200 mm 2 flexible substrate, with a system throughput of 3 mm/s. The patterning yield is quantitatively analyzed by an automated electron beam inspection method, demonstrating longterm repeatability of an up to 88% yield over a 4-month period. The inspection method can also be employed to examine pattern uniformity, achieving an average yield of up to 78.6% over full substrate areas. The proposed patterning method is highly versatile and scalable as a nanomanufacturing platform and can find application in nanophotonics, nanoarchitected materials, and multifunctional nanostructures.