The main goal of this study is to use effective microorganisms as a probiotic to improve the ability of tilapia fish to cope with temperature stress and heavy metal exposure. The experiment design was split block, incorporating three temperature levels (24°C, 28°C, and 32°C) and three different heavy metals (CuSO4, CdCl2, and Pb (NO3)2), and the duration of the experiment was two weeks. All stages groups included effective microorganisms (EM) groups in comparison with treatment groups. Quantitative real-time PCR (qRT-PCR) was used to follow the expression profiles of heat shock proteins (HSP70, HSP27, and HSP90) genes in Nile tilapia fish. Moreover, the activities of antioxidant enzymes catalase (CAT) and glutathione-S-transferase (GST) were examined in fish liver. Expression levels in HSP27 and HSP 90 genes were increased significantly (p< 0.05) in fish groups treated with CuSO4 at all temperature levels while expression levels of HSP70 gene increased significantly (p< 0.05) in the fish group treated with CuSO4 at 28°C. At the same time, results varied in CdCl2 treatment with variations in temperature. But in case of Pb(NO3)2 stage, expression levels in HSP27 gene increased significantly (p< 0.05) in fish groups subjected to (24°C and 28°C), while increased in the HSP70 gene significantly (p< 0.05) in fish groups subjected to (24°C and 32°C). Results of antioxidants enzymes revealed that, the decrease in their activities was more detectable in the groups exposed to 0.1LC50 of (Cu, Cd, and Pb) at the most temperatures levels. Results proved the positive impact of effective microorganisms on tilapia fish immunity and adaptation to climate change in aquaculture. As a recommendation EM could be used in fish farms to enhance fish productivity and reduce the toxic effects of pollutants.