The invention discloses a method for preparing a semiconductor nanostructure through directional self-assembly and mask regulation and control. The method comprises: forming a double-layer hard mask layer, a photoetching stacking layer and a buffer layer on a semiconductor substrate, spin-coating a block copolymer (BCP) layer on the buffer layer, and annealing to form a self-assembly template pattern; removing a certain block then to form a photoetching pattern, sequentially transferring the pattern to a buffer layer, a photoetching stacking layer and a second hard mask layer, depositing a dielectric layer on the patterned second hard mask layer, flattening, removing the second hard mask layer then, and transferring the pattern to a first mask layer and a semiconductor substrate by takingthe patterned dielectric layer as a mask. According to the method, the problem of directional self-assembly caused by the thickness of the block copolymer and low etching selectivity among different block molecules in the existing pattern transfer process can be greatly solved.