The present invention is a method of fabricating a self-aligned split gate of flash memory. Aligned layers are formed on predetermined source regions and predetermined drain regions in advance. Spacers are formed on the sidewalls of the aligned layers. An etching rate of the spacers is different from an etching rate of the aligned layers. Therefore, if misalignment occurs during the patterning process to form a split control gate layer, the spacers also can be left after the aligned layer is removed. The remaining spacers serves as a implant mask during the implantion for the sources and the drains formation, so that the sources and the drains are formed in the respective positions of the aligned layers by self-alignment.