A new class of Ni(dmit)(2) anion radical salt (Et-2,5-DBrP)[Ni(dmit)(2)](2) (1) (Et-2,5-DBrP = ethyl-2,5-dibromopyridinium) was developed. Single-crystal X-ray diffraction analysis indicates that this salt contains two crystallographically independent anion layers in the crystal with effective Br center dot center dot center dot S halogen bonds between the cation and the anion. The crystal and electronic structures, and electrical and magnetic measurements reveal that 1 is a novel bilayer Mott system, in which two different Mott-insulating anion layers coexist in one crystal. Selective halogen substitution of Br with I at the 2-position in the cation affords the isostructural bilayer salt (Et-2I-5BrP)[Ni(dmit)(2)](2) (2) (Et-2I-5BrP = ethyl-2-iodo-5-bromopyridinium), while substitution at the 5-position results in a structural change, yielding the monolayer salt (Et-2Br-5IP) [Ni(dmit)(2)](2) (3) (Et-2Br-5IP = ethyl-2-bromo-5-iodopyridinium). These results indicate that the halogen bond plays an important role to realize the bilayer system, and that the crystal structure is controlled by tuning the strength of the halogen bond. The low temperature magnetic properties of the two isostructural salts 1 and 2 are significantly different, because they are affected by fluctuated spins that do not participate in the formation of short-range antiferromagnetic domains. The bilayer salt generates the fluctuated spins more easily than conventional monolayer salts, and such fluctuated spins are expected to result in unique physical properties.