The appearance of phase segregations in the kesterite Cu2ZnSn(Sx,S1−x)4 (CZTSSe) absorber layer and formation of the interfacial Mo(S,Se)2 layer during the annealing process is a challenge and limitation for the inderstrization of highly efficiency and low-cost thin film solar cells (TFSCs). These two factors are effectively controlled by sulfurization temperature. In this study, kesterite CZTSSe thin films were successfully prepared via the sulfurization of co-evaporated Cu–Zn–Sn–Se precursor, which was deposited on Mo-coated glass substrates at sulfurization temperatures ranging from 520 °C to 580 °C. The structure and phase of the sulfurized CZTSSe films were characterized by conventional XRD and Raman analyses. The thickness of the Mo(S,Se)2 layer was estimated based on cross-sectional FE-SEM images. Advanced characterizations, such as STEM images and STEM EDS analyses of the sulfurized CZTSSe films were performed to detect the sulfurization temperature dependent phase segregation and localized fluctuations in the elemental composition of the sulfurized CZTSSe films. The formation of secondary phases was clearly evident at the bottom region in the CZTSSe absorber thin films prepared over sulfurization temperature of 540 °C. The performances of the devices were strongly related to the sulfurization temperature, thickness of the interfacial Mo(S,Se)2 layer and proportion of secondary phases in the kesterite CZTSSe absorber layers. The highest power conversion efficiency was 5.52% and was achieved by the CZTSSe absorber layer prepared at 540 °C (Voc:0.575 V, Jsc:18.14 mA/cm2 and FF: 52.94%).