The invention provides a method which can improve the breakdown voltage between two adjacent N wells; the two adjacent N wells are manufactured in a silicon substrate and a shallow trench isolation structure is arranged between the two adjacent N wells; the depth of the two adjacent N wells is larger than that of the shallow trench isolation structure; and the two adjacent N wells are isolated byan upper-layer isolation well P which is arranged below the shallow trench isolation structure. In the prior art, the position of an ion concentration peak value of the two adjacent N wells is deeperthan that of the upper-layer isolation well P, therefore, leak current can punch through the silicon substrate between the two adjacent N wells, thereby leading the leaked current to be excessively large and the breakdown voltage to be too small. The method can form a lower-layer isolation well P below the upper-layer isolation well P by the ion injection process. By adopting the invention, the leak current between the two adjacent N wells is changed to be led by a PN junction leak current from the put-through current between the N wells, thereby reducing leak current between the two adjacentN wells, and greatly improving the breakdown voltage between the two adjacent N wells, and simultaneously maintaining the electrology characteristic of the device.