The invention relates to a preparation method of high viscosity cationic starch, which comprises the technological steps of: 1) using the mixture of an alkaline catalyst and an inhibitor to adjust the pH of starch slurry to be 10swung dash12; 2) heating and adding the mixture of an alkaline activating agent and a cationic etherifying agent, and stopping heating until the temperature reaches 40 DEG C; 3) using the mixture of the alkaline catalyst and the inhibitor to adjust the pH of the starch slurry to be 11swung dash12, keeping heating until the temperature of the starch slurry reaches 49swung dash50 DEG C, and etherifying for 1swung dash5h; 4) adding an alkaline cross-linking agent, and reacting for 1swung dash6h; and 5) dehydrating the starch slurry, obtaining green starch, adding an acidulant, mixing uniformly, acidizing the starch for 0.5swung dash2h at 50swung dash100 DEG C, and after cooling, smashing and screening, obtaining a product. The product has high paste viscosity, high acid and alkaline-resistant stabilities, and can be applied in the fields of paper making, mineral separation, oil fields, adhesives, waste water treatment and the like.