In this work, stable Cu2ZnSnS4 (CZTS) nanocrystals (NCs) in pure kesterite phase were synthesized by a facile one-pot rapid injection technique (colloidal route). Time-dependent reaction mechanism for the synthesis of CZTS nanoparticles is explained. When TOP-S (Tri-octyl phosphine–sulphur) was injected in the CuZnSn-complex with TOPO (Tri-octyl phosphine oxide) as capping ligand, orthorhombic phase Cu2−XS nanoparticles of spherical shape were found at nucleation sites. With an advancement in the reaction time, Sn got infused in Cu2−XS to form Cu2SnS3 and its shape got deformed. Further increase in reaction time infuses Zn to form Cu2ZnSnS4 with the gradual vanishing of Cu2−XS and Cu2SnS3 phases and finally, the rod-shaped CZTS Np’s were obtained. This factor of reaction time, which influence the morphology and size were studied in detail. The structural and optical properties of the pure kesterite phase CZTS nanorods were also analysed. The band gap of the rod-like CZTS is determined to be around 1.43 eV, which is an optimum value for solar photoelectric conversion.