A self-alignment method for a recess channel dynamic random access memory includes providing a substrate with a target layer, a barrier layer and a lining layer, wherein the target layer has shallow trench isolation structures; patternizing the lining layer, barrier layer and target layer to form recess trench channels; depositing a dielectric layer onto the recess trench channel; forming an ion doped region in the target layer; removing a portion of the dielectric layer to expose a portion of the recess trench channel; forming a filler layer covered onto the recess trench channel; removing a portion of the filler layer to expose a portion of the recess trench channel; forming a passivation layer onto the recess trench channel; removing the passivation layer on the lining layer; and removing the lining layer to form a plurality of structural monomers disposed at the recess trench channel and protruded from the target layer.