Abstract To evaluate uncertainty in the transient climate response (TCR) associated with microscale deep-ocean mixing processes induced by internal tidal wave breaking, a set of idealized climate model experiments with two different implementations of deep-ocean mixing is conducted under increasing atmospheric CO₂ concentration 1% per year. The difference in TCR between the two experiments is 0.16 °C, which is about half as large as the multimodel spread of TCR in the Fifth Assessment Report of the Intergovernmental Panel on Climate Change. The TCR difference can be attributed to the difference in the preindustrial climatological state. In the case where deep-ocean mixing works to enhance ocean stratification in the Pacific intermediate-to-deep layers, because the Pacific water mass is transported to the Southern Ocean by the Pacific meridional overturning circulation, the subsurface stratification in the Southern Ocean is also enhanced and deep wintertime convection there is suppressed. Our study shows that in this case during CO₂ increase, ocean heat uptake from the atmosphere to deeper layers is suppressed and TCR is estimated to be higher than the other case. Diminished accumulation of oceanic heat in the deep layer also leads to the sea level depression of ∼0.4 m in the Southern Ocean when atmospheric CO₂ concentration has quadrupled. Together with convective and cloud-radiative processes in the atmosphere and oceanic mesoscale processes, microscale deep-ocean mixing can be one of the major candidates in explaining uncertainty in future climate projections.