This paper presents the morphological capillary-porous structure analysis of sunflower seed, using X-ray microtomography in the longitudinal and transverse section and FESEM analysis of the surface microstructure after novel technologies treatment. Two types of treatment are considered: pulsed electric field treatment that has electroporation effect of the oil cell structure and pulsed microwave treatment that affects the internal structure. The main characteristic of the capillary-porous structure of oil-bearing material is given. Air cavities in the structure of the sunflower kernels were observed using X-ray microtomography. The influence of a pulsed electric field treatment on structure integrity of sunflower cells has been obtained with the creation of a material that has a greater permeability for diffusion processes. Experimentally was determined that over 2500 electric pores were formed on an area of 1 cm2 as a result of a pulsed electric field treatment. In the case of a pulsed electric field treatment, the oil seed body model can be represented as a bi-dispersed structure with the addition micro capillaries, formed by an electric field. It was experimentally defined that pulsed microwave treatment affected of internal seed structure. Denaturation of proteins and breakage of oil globules after pulsed microwave treatment decreased dispersion of the sizes of particles approximately twice with 35.3 μm2 up to 18.1 μm2. The data obtained are of interest not only for the technology of processing oilseeds but also for the analysis of novel emerging technologies.