The thermometer in a distillation setup is used to monitor and control the temperature of the distillation process. It helps to ensure that the desired compounds are being separated at the correct temperature and that the distillation is proceeding efficiently. By monitoring the temperature, the operator can make adjustments to the heat source to maintain the desired temperature range for the separation of components. This helps to prevent overheating or underheating of the mixture, which could result in incomplete separation or degradation of the compounds being distilled.