The scattering of X-ray ultrashort pulses (USPs) is an important aspect of the diffraction analysis of matter using modern USP sources. The theoretical basis, which considers the specifics of the interaction of ultrashort pulses with complex polyatomic structures, is currently not well developed. In general, research is focused on the specifics of the interaction of ultrashort pulses with simple systems—these are atoms and simple molecules. In this work, a theory of scattering of X-ray ultrashort pulses by complex polyatomic structures is developed, considering the specifics of the interaction of ultrashort pulses with such a substance. The obtained expressions have a rather simple analytical form, which allows them to be used in diffraction analysis. As an example, it is shown that the obtained expressions can be used to study the structures of deoxyribonucleic (DNA) and ribonucleic (RNA) acids.