AbstractThe title nonplanar electron acceptor (1) fused with a selenadiazole ring selectively forms a crystalline charge‐transfer complex (CT crystal) with 2,6‐dimethylnaphthalene (2,6‐DMN). On the other hand, the sulfur analogue (2) has less recognition ability and forms CT crystals with both 2,6‐ and 2,7‐DMN. X‐ray analyses of 1, 2, and their CT crystals revealed that the Se⋅⋅⋅N chalcogen bond (ChB) in 1 is strong enough to determine the crystal packing with the formation of a cavity suitable for 2,6‐DMN. On the contrary, ChB through S⋅⋅⋅N contact in 2 competes with other weak interactions such as a C−H⋅⋅⋅N hydrogen bond. The stronger ChB involving Se is the key for 1 to separate 2,6‐DMN (>97 wt %) from a complex isomer mixture containing ca. 10 wt % each of 2,6‐ and 2,7‐DMN by a simple, efficient and straightforward mixing‐filtration‐heating process.