Kesterite-based copper zinc tin sulfide (CZTS) and copper zinc tin selenide (CZTSe) thin films have attracted considerable attention as promising materials for sustainable and cost-effective thin-film solar cells. However, the successful integration of these materials into photovoltaic devices is hindered by the coexistence of secondary phases, which can significantly affect device performance and stability. This review article provides a comprehensive overview of recent progress and challenges in controlling secondary phases in kesterite CZTS and CZTSe thin films. Drawing from relevant studies, we discuss state-of-the-art strategies and techniques employed to mitigate the formation of secondary phases. These include a range of deposition methods, such as electrodeposition, sol-gel, spray pyrolysis, evaporation, pulsed laser deposition, and sputtering, each presenting distinct benefits in enhancing phase purity. This study highlights the importance of employing various characterization techniques, such as X-ray diffraction, Raman spectroscopy, scanning electron microscopy, and energy-dispersive X-ray spectroscopy, for the precise identification of secondary phases in CZTS and CZTSe thin films. Furthermore, the review discusses innovative strategies and techniques aimed at mitigating the occurrence of secondary phases, including process optimization, compositional tuning, and post-deposition treatments. These approaches offer promising avenues for enhancing the purity and performance of kesterite-based thin-film solar cells. Challenges and open questions in this field are addressed, and potential future research directions are proposed. By comprehensively analyzing recent advancements, this review contributes to a deeper understanding of secondary phase-related issues in kesterite CZT(S/Se) thin films, paving the way for enhanced performance and commercial viability of thin-film solar cell technologies.