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To develop a new spin-crossover functional material, a magnetic hybrid compound [Fe(qsal)2][Ni(mnt)2] was designed and synthesized (Hqsal = N-(8-quinolyl)salicylaldimine, mnt = maleonitriledithiolate). The temperature dependence of magnetic susceptibility suggested the coexistence of the high-spin (HS) Fe(III) cation and π-radical anion at room temperature and a magnetic transition below 100 K. The thermal variation of crystal structures revealed that strong π-stacking interaction between the π-ligand in the [Fe(qsal)2] cation and [Ni(mnt)2] anion induced the distortion of an Fe(III) coordination structure and the suppression of a dimerization of the [Ni(mnt)2] anion. Transfer integral calculations indicated that the magnetic transition below 100 K originated from a spin-singlet formation transformation in the [Ni(mnt)2] dimer. The magnetic relaxation of Mössbauer spectra and large thermal variation of a g-value in electron paramagnetic resonance spectra below the magnetic transition temperature implied the existence of a magnetic correlation between d-spin and π-spin.