Selective metal Mg deposition was achieved for a structure with the 8-nm-thick intermediate layer of Alq3 on a photochromic diarylethene (DAE) layer. Selective deposition for a structure with the Alq3 intermediate layer was attributed to uncolored DAE molecules exposed on the surface due to the migration and the aggregation of Alq3 molecules on the uncolored DAE layer. Laser spot irradiation enables both isomerization and an annealing effect on samples with an Alq3 intermediate layer, thereby achieving selective Mg deposition. Selective deposition for a structure with an intermediate layer could be important for the preparation of patterned cathodes in the field of organic electronics.