We investigate the role of mesoscale organization for the response of trade cumulus (Tc) clouds to climate change. Among four recently identified states of Tc organization, the “Sugar” state has the lowest and the “Flower” state the highest cloud fraction and cloud radiative effect. Using large‐eddy simulations, we find that the Flower Tc state is more sensitive to climate change than the Sugar Tc state. In the considered case, the short‐wave cloud radiative effect weakens by 0.28 W m−2 in the Sugar state and by 1.5 W m−2 in the Flower state over the course of 21st century under the RCP8.5 emissions scenario. This is accompanied by a reduction of the short‐wave cloud radiative effect variance on the mesoscale. The primary mechanism is stabilization of the boundary layer by stronger long‐wave radiative heating at the inversion associated with higher greenhouse gas levels. This weakens the boundary layer mesoscale circulation that is responsible for aggregation of moisture and formation of the Flower Tc state. Thus, in the considered case, organization on the mesoscale amplifies the positive feedback of Tc clouds to climate change. Owing to the widespread occurrence of boundary layer mesoscale circulations in the Tc regime, this mechanism could modulate the Tc response to climate change in general.