The most reported stable crystal structure of Cu2ZnSnS4 and Cu2ZnSnSe4 (CZTSe) is kesterite, which is derived from the ternary chalcopyrite structure. However, by controlling the reaction conditions, we found that the structure and composition of the CZTSe nanocrystals (NCs) can be tuned. This can be achieved by using a simple hot injection approach. The structural properties of the CZTSe NCs were characterized by powder X-ray diffraction (PXRD), Raman spectroscopy and transmission electron microscopy. The energy dispersive X-ray spectroscopy confirms the stoichiometry of CZTSe NCs. The optical band gap of the NCs is found to be around 1.38 eV, as estimated from UV-Vis absorption spectroscopy. PXRD studies show that the obtained CZTSe NCs occurring in three structurally different phases (tetragonal kesterite type, hexagonal wurtzite type and orthorhombic wurtz-stannite type) are converted to the kesterite structure by annealing at 540 °C for 30 min under an Se-vapour atmosphere.