There is provided an optical encoder with alignable relative positions between elements including an encoding medium, a sensor package and a memory. The sensor package includes a photodiode array and two alignment photodiodes opposite to the encoding medium. The memory records an alignment pattern associated with output signals of the two alignment photodiodes when the encoding medium and the sensor package are at nominal operating positions. When the encoding medium and the sensor package are not at the nominal operating positions, the relative position alignment is performed by adjusting current relative positions between the encoding medium and the sensor package to cause a current pattern associated with output signals of the two alignment photodiodes to be identical to the alignment pattern.