CO2 flux in dryland ecosystems is typically limited by soil carbon release, resulting in pulses of flux with precipitation and transitions between low and high moisture. Soil crack morphology, which shifts distinctly between these wet and dry periods, can introduce additional complexity to the magnitude and dynamics of CO2 flux, though its full effects remain unknown. In this study, we combine analyses of minute-scale temperature profile fluctuations in a model soil fracture with CO2 flux measurements in Kenyan vertisols with known differences in crack morphology. We show that flux enhancements due to crack morphology are due to thermal convection and are driven by depth and aperture. Combined with elevated levels of carbon in the soil, fluxes can consistently increase several orders of magnitude. However, limitations imposed on either axis of soil mechanics or soil carbon release modulate the magnitude of CO2 flux and increase variability. Our results provide a stronger integration of the role that soil structure plays on dryland CO2 flux dynamics.