A method for semiconductor self-aligned patterning includes steps of providing a substrate comprising a first layer and a second layer, wherein the first layer is on top of the second layer; removing a portion of the first layer to form a first pattern; depositing a first conformal layer on the first pattern; depositing a second conformal layer on the first conformal layer; removing a portion of the second conformal layer to expose a portion of the first conformal layer; and thinning the first conformal layer and the second conformal layer alternatively to form a second pattern. A semiconductor self-aligned structure is also provided.