A method for preparing a flash memory structure comprises the steps of forming a plurality of dielectric blocks having block sidewalls on a substrate, forming a plurality of first spacers on the block sidewalls of the dielectric blocks, removing a portion of the substrate not covered by the dielectric blocks and the first spacers to form a plurality of trenches in the substrate, performing a deposition process to form an isolation dielectric layer filling the trenches, removing the dielectric blocks to expose spacer sidewalls of the first spacers, forming a plurality of second spacers on the spacer sidewalls of the first spacers, and removing a portion of the substrate not covered by the first spacers, the second spacers and the isolation dielectric layer to form a plurality of second trenches in the substrate.