The changes in biomass (including yield), copper (Cu) concentration, and the accumulation of wheat (Triticum aestivum. L) in response to soil Cu pollution under nighttime warming had still not been explored. Hence, this study was carried out, and these variations were analyzed from a physiological perspective. Pot trials were performed at two levels of ambient temperatures (no-warming (NT) and average nighttime warming of 0.28 °C (WT)) and two levels of soil Cu concentrations (control check without Cu application (CK) and 100 mg/kg Cu application (Cu)). Soil was collected from the carbonate cinnamon soil region of central China. The warming effects of the passive nighttime warming system were prominent, and the average increment was 0.28 °C. Antioxidant enzyme activities were promoted by warming (p < 0.05) and Cu. The highest yield was achieved in NT-Cu, mainly attributed to relatively strong root activity and photosynthesis caused by supplemental Cu, but the Cu concentration in its grains was close to the threshold (10 mg/kg) for Cu concentration in foodstuff and could present a potential food safety risk. Though nighttime warming did not increase the total biomass and yield of wheat, it decreased the Cu accumulation of wheat grown in Cu-contaminated soil, especially in grains. Moreover, WT-CK and WT-Cu increased the Cu concentration in the roots and glumes and reduced the Cu concentration in grains by 13.09% and 55.84%, respectively, probably because of a lower transpiration rate. Among them, the Cu concentration of grains in WT-Cu was the lowest and significantly lower than other applications. Our findings reveal that nighttime warming has the potential to reduce the Cu risk of grains in wheat grown in the Cu-contaminated carbonate cinnamon soil region of central China and could then provide a theoretical reference for risk assessment of food quality for wheat subjected to dual stress from nighttime warming and Cu pollution.