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Cultures of Scytonema javanicum obtained from artificial medium are used to control desertification, and through the effective redistribution of nutrients, related environmental problems can be alleviated. Wastewater is considered to be a potential alternative medium for S. javanicum. However, the effect of temperature on the nutrient redistribution ability of S. javanicum cultured in wastewater has rarely been considered. Therefore, this study explores the effect of temperature on S. javanicum in wastewater. The results showed that a sufficient temperature increase (from 25 °C to 30 °C) increased the photosynthetic activity of photosynthetic system II (PSII), accelerated the accumulation rate of S. javanicum biomass, and improved the removal efficiency of nutrients in wastewater. However, an increasing temperature caused a decrease in the final accumulated biomass. When the temperature was above 35 °C, the ratio of the variable to maximal fluorescence (Fv/Fm) of S. javanicum decreased, thus, causing damage to PSII. The average Fv/Fm at 35 °C and 40 °C decreased by 10.49% and 72.37%, respectively, compared to that at 25 °C. By analysing the chlorophyll fluorescence induction kinetics (OJIP) curve after 30 days, the P phase at 30 °C increased by 15.47% relative to that at 25 °C, whereas that at 35 °C and 40 °C decreased by 45.54% and 86.37%, respectively. In particular, at 40 °C, the O-J-I-P phase transformed into the O-J (J = I = P) phase, which caused irreversible damage to the PSII of S. javanicum. Comprehensive scores were determined using the entropy weight method and revealed that 30 °C was the optimal temperature for the wastewater culture of S. javanicum. This temperature improved the biomass accumulation rate and wastewater transfer efficiency. These results provide a scientific basis for improving the efficiency of the coupling technology of wastewater treatment and desert algal cultivation. Unlabelled Image • Accelerating the transformation of wastewater pollution to desert resources. • Increasing the temperature (< 35 °C) can accelerate biomass accumulation and nutrient redistribution. • The time to reach the maximum biomass at 30 °C was shortened to 25d. • Temperature exceeding 35 °C will cause serious damage to PSII system. • 30 °C is more suitable for long-term operation (> 150 d). [ABSTRACT FROM AUTHOR]