The cloud temperature is, as it sounds, the temperature of a cloud. However, what this means exactly depends on how the measurement is made. Most of the time we do not put a thermometer in the cloud, but instead determine this by remote sensing. And most clouds are not at a single temperature, but are generally colder at the top and warmer at the bottom. The temperature measured by remote sensing is often called a cloud effective temperature. It measures the temperature of the cloud mass within about 1 optical depth of the edge (where optical depth varies with wavelength, so that the measured temperature depends on the sensor being used, at least to some extent).

Measurements made from orbit, then, will generally measure a lower temperature than those made from the ground (unless the cloud is thin)