We investigated the local disordered layer in stannite nanocrystals by using a magnetic phase analysis and Mossbauer spectroscopy. Stannite nanocrystals were synthesized by using high-temperature to prevent precipitation in a coordinating solvent, oleylamine, at reaction temperatures of 230, 280, and 330 °C to induce local changes in crystallization. Magnetic susceptibility measurements revealed that antiferromagnetic ordering became weaker as the reaction temperatures were decreased. These results indicate the presence of Fe3+ clusters originating from the emergence of a disordered Cu+Fe layer at low reaction temperatures, and this disordered Cu+Fe layer induced the change observed in the band-gap energy of the stannite nanocrystals.