Studying the effect of microwave fields on the intensification of heat and moisture exchange processes in a granular layer is a rather complicated task, which cannot be effectively solved without an adequate research methodology. In presented materials, a system of principles and approaches for studying processes of microwave-convective grain treatment has been discussed. Based on the explicitly defined process target, functional-physical analysis has been performed that made it possible to specify the most essential factors of process. Morphological analysis of processes shall be performed in several stages. At each stage, targets of process have to be set by excluding combinations of factors that have no reason to be considered at this particular stage of process development. Application of mathematical simulation methods is advisable for selection of optimal options.