The physicochemical conditions of the siliconizing and boron–siliconizing processes of molybdenum-based alloys in a closed reaction space in an environment of chlorine and fluorine at reduced pressure were studied. Theoretical calculations of the equilibrium composition of systems with the participation of silicon, boron, molybdenum, nitrogen, oxygen, chlorine, and fluorine were carried out, which made it possible to determine the influence of process parameters (temperature, composition of the reaction medium) on the probable phase composition of the obtained coatings. Based on thermodynamic calculations, the composition and rational consumption of the initial powders and the temperature intervals of the chemical heat treatment (CHT) during the complex saturation of molybdenum-based alloys with silicon and boron were modeled. It was established that it is advisable to use chlorine as an activator, which leads to the formation of molybdenum chlorides MoCl4 and MoCl3 in the composition of the gas phase and can indicate the flow of exchange reactions between chlorides and the matrix of the processed material in the reaction space. The rational saturation temperature of alloys based on molybdenum with silicon and boron is determined—1100–1250 °C. The possibility of the existence of condensed phases MoSi2, MoB2.15, B6Si, MoB1.65, and MoB is shown.