Multinary sulfides represent a significant family of semiconductors because of their low cost and promising performance, yet controlling their composition is challenging. CuFeS2 thin films are particularly attractive because of their great potential in thermoelectricity and photovoltaics. Herein we reveal the newest finding that Zn promotes the cation ordering and stabilizes the chalcopyrite CuFeS2 film, preventing the reverse transformation to wurtzite with a random distribution of Cu–Fe at high temperature. The thermoelectric properties of chalcopyrite thin films are investigated as a function of Zn content, resulting in an optimized power factor of 0.168 mW/m·K2 at room temperature, outperforming any CuFeS2 thin films ever reported. For the first time, synchrotron-based in situ X-ray diffraction and X-ray absorption fine structure confirm the phase transition, offering insights into the isomeric structure of CuFeS2 and the role of Zn. The in-depth understanding of cation-ordering and phase transformation between CuFeS2 polymorphs might impact the multinary sulfide film fabrication and improvement in efficiency of renewable energy applications.