Nanocontainers have great potentials in targeted drug delivery and nanospace-confined reactions. However, the previous synthetic approaches exhibited limited control over the morphology, size and materials of the nanocontainers, which are crucial in practical applications. Here, we present a synthetic approach to multi-segment linear-shaped nanopores with pre-designed morphologies inside anodic aluminium oxide (AAO), by tailoring the anodizing duration after a rational increase of the applied anodizing voltage and the number of voltage increase during Al foil anodization. Then, we achieve nanocontainers with designed morphologies, such as nanofunnels, nanobottles, nano-separating-funnels and nanodroppers, with tunable sizes and diverse materials of carbon, silicon, germanium, hafnium oxide, silica and nickel/carbon magnetic composite, by depositing a thin layer of materials on the inner walls of the pre-designed AAO nanopores. The strategy has far-reaching implications in the designing and large-scale fabrication of nanocontainers, opening up new opportunities in nanotechnology applications.