Thermal control materials are employed to adjust the temperature of a spacecraft operating in deep space. The spectral emissivity is a crucial factor in evaluating the thermal radiative properties of such materials. An apparatus, composed of a Fourier transform infrared spectrometer (FTIR), a sample cooling chamber and a mechanical modulation system was demonstrated to measure low temperature infrared spectral emissivity under vacuum. The mechanical modulation system, which includes a chopper and a lock-in amplifier, is employed to reduce the interference of background radiation during measurements. The limitation of the Fourier transform frequency on the chopper frequency can be eliminated by setting the FTIR on step-scan mode. The apparatus is separated into two parts and evacuated by different pumps. In this study, a high quality emission spectrum of a sample is measured by the apparatus. The spectral emissivity of thermal control materials are obtained in the wavelength range of 8 to 14 μm at 173 and 213 K. The combined standard uncertainty of the apparatus is 3.30% at 213 K.