A method is described for directly measuring the temperature of a substrate in a molecular-beam epitaxy (MBE) growth system. The approach relies on the establishment of the temperature dependence of Raman-active phonons of the substrate material using independently known calibration points across the range of interest. An unknown temperature in this range is then determined based on the Raman peak position with the substrate in situ the MBE chamber. The apparatus relies on conventional optics and Raman components. Shifting and broadening of the Raman spectrum are described based on the effects of thermal expansion and anharmonic decay. The choice of reference temperature is discussed. The method is qualified by examining the substrate temperature dependence, relative to that of a standard thermocouple, during a commonly used ramp procedure. Both temperature difference and time lag are obtained.