The invention discloses a cationic polyacrylamide flocculant with a micro-blocking structure, and a preparation method and an application of the flocculant. The preparation method comprises the stepsof mixing an acrylamide monomer solution, a cationic monomer copolymerized with an acrylamide monomer, an anionic polymer as a template molecule, urea and EDTA (ethylene diamine tetraacetic acid) to form acrylamide prepared solution and then giving a template polymerization reaction under a composite initiation system comprising K2S2O8-NaHSO3-V50. The flocculant is relatively high in flocculationrate in a high temperature and high acid environment, has a good solid-liquid settlement separation effect and therefore, solves the problem that an appropriate flocculant cannot be found in an aluminum oxide production technology of a settlement tank system by a one-step acid solution method.