In this study, the effect of depositing CdSeTe and CdTe layers at different substrate temperatures (STs) by evaporation in vacuum on the properties of the CdSeTe/CdTe stacks was investigated. First, CdSeTe layers in stack structure were grown at STs of 150 °C, 200 °C and 250 °C and then CdTe layers on the CdSeTe produced with the optimum temperature were coated at STs of 150 °C, 200 °C and 250 °C. The employing of STs up to 150 °C on both CdSeTe and CdTe films in CdSeTe/CdTe stacks demonstrated the presence of Te and/or oxide phases as well as the alloying, while more stable phase structures at higher temperatures. In the CdSeTe/CdTe stack, the increase in ST of CdSeTe promoted the alloying, while it weakened the alloy in which was applied in CdTe. It was concluded that under the applied experimental conditions, STs of 250 °C and 200 °C with the graded alloying structure, suitable absorption sites, more homogeneous surface morphology for potential solar cell applications would be more suitable for CdSeTe and CdTe, respectively. As a result, the application of ST to CdSeTe or CdTe in the stacks can be used as a tool to control the properties of the stack structure.