Composition engineering and size alteration have been employed as the traditional routes for tuning chemical and physical properties semiconductor nanocrystals. Phase transformation of nanocrystals leading to the change in size/shape/composition of the nanocrystals is attractive tool as well as it opens new possibilities for the fabrication of micro structured optoelectric devices and semiconductor films with controlled morphology. Till date, induced phase transformation in semiconductor nanocrystals has been achieved by doping, pressure or high temperature (> 450 °C) treatment of phase pure nanocrystals. Herein, we demonstrate the structural phase transition of complex quinary system of Cu₂ZnSn(SSe)₄ (CZTSSe) from metastable wurtzite form nanocrystals into most stable kesterite CZTSSe grains via solution based post-treatment approach. The structural transition in this complex quinary system could be achieved via two different transition routes depending on the reaction parameters employed during the synthesis of wurtzite-derived nanocrystals. The wurtzite CZTSSe nanocrystals synthesized with OLA (as the only coordinating solvent and ligand) undergo two intermediate stages before transforming into kesterite phase grains, when post-treated with combination of ligands. They first transform into wurtzite-zinc blende derived polytypic nanocrystals at lower temperatures and are modified into pure phase zinc blende particles with the further progression of reaction. These zinc-blende derived particles are stable for a long range of temperature and could be stabilized in kesterite phase via annealing the particles at high temperatures. When the wurtzite nanocrystals are synthesized via using non-coordinating solvent (ODE) and TOPO and are injected in the post-treatment flask, they are directly transformed into the final stable kesterite phase without undergoing a ZB-derived intermediate phase formation. To confirm the transitional temperature of the fast phase transition, ex-situ annealing (hot plate) and in-situ annealing (High temperature XRD chamber) has been performed. The shape, composition and band gap change at different stages of the chemically and thermally induced phase transformation has been subsequently investigated with transmission electron microscopy (TEM), X-ray diffraction (XRD), energy dispersive X-ray analysis (EDX), UV-vis-NIR techniques and cyclic voltammetry (CV).