The theory of scattering of ultrashort laser pulses (USP) is the basis of diffraction analysis of matter using modern USP sources. At present, the peculiarities of interaction of USP with complex structures are not well developed. In general, the research focuses on the features of the interaction of USP with simple systems, these are atoms and simple molecules. Here we present a theory of scattering of ultrashort laser pulses on molecules with a multi-atomic structure, taking into account the specifics of the interaction of USP with such a substance. The simplicity of the obtained expressions allows them to be used in diffraction analysis. As an example, the scattering spectra of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are presented. It is shown that the theory developed here is more general in the scattering theory and passes into the previously known one if we consider the duration of the USP to be sufficiently long.