For successful long-term deployment and operation of kesterites Cu2ZnSn(SxSe1−x)4 (CZTSSe) as light absorber materials for photovoltaics, device stability and recovery in kesterite solar cells are investigated. A low temperature heat treatment is applied to overcome the poor charge extraction that developed in the natural aging process. It is suggested that defect states at aged CZTSSe/CdS heterojunctions were reduced while apparent doping density in the CZTSSe absorber increased due to Cd/Zn inter-diffusion at the heterojunction during the annealing process. In situ annealing experiments in a transmission electron microscope were used to investigate the elemental diffusion at the CZTSSe/CdS heterojunction. This study reveals the critical role of heat treatment to enhance the absorber/Mo back contact, improve the quality of the absorber/buffer heterojunction and recover the device performance in aged kesterite thin film solar cells.