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Chronic heat stress caused by global warming can have serious implications for fish survival. The kidney plays a central role in many homeostatic functions, including water and electrolyte regulation. However, there is limited knowledge about the effect of heat stress on fish kidneys. In this study, water temperatures were increased from 20 °C to 24 °C and 28 °C in 8 days at a warming rate of 1 °C/d, and then maintained for 12 days. We investigated the effects of mild heat stress (24 °C) and high heat stress (28 °C) on Siberian Sturgeon (<i>Acipenser baerii</i>) kidneys using histological observation, flow cytometry detection, and RT-qPCR. Our histological observations revealed that heat stress caused significant infiltration of inflammatory cells in the kidney, especially at 28 °C. The flow cytometry assay demonstrated a significant increase in the number of apoptotic cells after heat stress at 28 °C compared to a control group at 20 °C (<i>p</i> = 0.033). The level of plasma creatinine was significantly increased in the 28 °C group compared to the control group (<i>p</i> = 0.001). In addition, the mRNA expression levels of heat shock protein <i>GRP75</i> increased (<i>p</i> = 0.009). The results indicate that heat stress at 28 °C caused damage to the kidneys of <i>A. baerii</i> and triggered the protective response of heat shock proteins. In conclusion, this study contributes to the understanding of the coping strategies of the kidney of <i>A. baerii</i> for chronic heat stress.