This study evaluates the dynamics of heat zones in the load and its relationship with the stress of pigs during transport. Four journeys of 170 km were monitored, recording the physiological variables of 192 animals (48 per journey), namely rectal temperature (RT), body temperature (BT), respiratory rate (RR), blood lactate concentrations and salivary cortisol. Heat zones and ventilation patterns were characterized by the spatial variability of the enthalpy and the Computational Fluid Dynamics of the load. The formation of a thermal core was observed in the frontal region of the load, which extended through the lower (LD) and upper (UD) decks. Pigs transported in the LD had higher means of RR (UD = 89 and LD = 94 breaths/min), and salivary cortisol (UD = 33.84 and LD = 34.92 ng/mL). The pigs transported in the UD presented the highest mean BT (UD = 38.9 and LD = 38.1 °C) and lactate (UD = 61.63 and LD = 58.26 mg/dL). Pigs transported in the LD of the load were more susceptible to thermal stress, while pigs transported in the UD showed greater physical stress and muscle exhaustion.