Recently, due to increasing environmental requirements, microwave carbonization method has been widely investigated for the production of activated carbon from biomass waste. Microwave carbonization is a more energy efficient and environmentally friendly method compared to traditional carbonization in thermal furnaces, but to date there are still a number of questions about the reproducibility and temperature stability of this process. During microwave irradiation, the temperature of biomass samples changes continuously and complex physical and chemical processes occur in them. For deeper study of these processes and determination of optimal modes of microwave treatment it is necessary to know the temperature dynamics of biomass samples. For this purpose, the method of spectral pyrometry based on the allocation of sections of the spectra of thermal radiation of samples coinciding with the Planck spectrum was used. In the specified spectral sections these samples are gray emitters. The method is effective for an unknown emission coefficient, continuously varying with changes in the microstructure, chemical composition and phase state of the sample. The sample irradiated by microwaves was a sample of orthophosphoric acid-treated cotton down weighing 1 g. The microwave source was a magnetron-type generator with a maximum output power of 600 W and an operating frequency of 2450 MHz. Thermal spectra of the irradiated sample were recorded by small-size spectrometers of visible (350–760 nm) and near-infrared (650–1050 nm) ranges. The time of irradiation of samples by microwaves was varied in the range of 60–180 s. To process the obtained spectra, the program “Spectral Pyrometry” was used, which reads the recorded spectrum, processes it, plots it in the necessary coordinates and calculates the temperature. Analysis of the obtained results revealed different types of thermal radiation spectra of the irradiated sample - spectra similar to spectra of a completely black body, spectra with different temperature zones of the sample, spectra with atomic lines and molecular bands. The results obtained are useful for the study of microwave influence on various objects, research of processes occurring during carbonization of biomass, as well as for the development of more effective modes of production of activated carbons by microwave method.