Application of nano-structures requires a knowledge of their fundamental physical (mechanical, electromagnetic, optical, etc.) characteristics. Thermodynamic properties associated with phonon displacements through the nano-samples are particularly interesting. Independent of the type of lattices, the thermodynamics of their subsystems (electrons, excitons, spin waves, etc.) is determined when the subsystem is in thermodynamic equilibrium with phonons. Phonons are collective mechanical oscillations of molecules or atoms and represent the most important system of excitations. Besides, the acoustical characteristics as well as conductive and superconductive properties etc. could not be realistically explained without phonons. All quoted is well known and all applications of phonons in bulk structures have been intensively exploited for more than a century. The fact which must be especially pointed out is that the role of phonons in nanostructures is much more impressive than in bulk structures. The main fact concerning phonon properties in nanostructures is the absence of the so-called acoustic phonons, i.e., phonons whose energy tends to zero when phonon momentum tends to zero. For the exciting of phonons in nanostructures activation energy different from zero is necessary. These unexpected characteristics require revision of all conclusions obtained by bulk theories of phonons. Therefore, the contribution of phonon subsystems to thermodynamic and energy transfering analysis is the first step in a research of nanostructure properties. This paper describes a major aspect of the effort to understand nanostructures, namely the study of phonons and phonon-mediated effects in structures with nanoscale dimensional confinement in one or more spatial dimensions. During the last two decades, there has been a steady effort to understand the optical and acoustic phonons in nanostructures such as the superlattice, quantum wires, nanotubes and quantum dots. The central theme of this paper is the description of the acoustic phonons of the optical type in these nanostructures. As a preliminary to describing the dispersion relations and mode structures for phonons in nanostructures, phonon amplitudes are quantized in terms of the harmonic oscillator approximation, and anharmonic effects leading to phonon decay are described in terms of the dominant phonon decay channels. These elastic and discontinued models are applied to describe the deformation potential and interactions in a variety of nanostructures. Dependence of energy on the wave vector is highly nonlinear and linear approximation of the laws of dispersion of phonons in small size nanostructures makes no sense. Changing the phonon dispersion law due to confinement severely affects the kinetic effects conditioned by the interaction of acoustic phonons with electrons, dotted defects, phonon-phonon interactions. Managing transport properties of acoustic phonons through the modification of their energy spectrum in nanostructures was named phonon engineering. In this paper we will try to observe the difference between the characteristics of different nano-crystalline structures: ultrathin films, composite films, i.e., superlattices, nanorods and quantum dots, we were interested in whether the quantum size effects (quantum confinement), quantum (de) coherence and influence of boundary conditions, strengthen or weaken in nanosamples. Finally, this paper describes how the dimensional confinement of phonons in nanostructures leads to modifications in the electronic, optical, acoustic, superconducting and thermodynamic properties of quantum. Thermal properties of nanostructures have recently attracted a lot of attention. The influence of size effects on thermal conductivity is becoming extremely important for device design and reliability. The problem of thermal management is even more severe for photonic devices such as vertical cavity surface emitting lasers. On the other hand, to improve performance of thermoelectrics, one needs to achieve low thermal conductivity. These are two contradictory demands, but both can be approached with appropriate modification of phonon modes, e.g., phonon engineering. On the basis of the calculated dispersion law and distribution of phonon states in nanoscopis crystals, free energy and entropy will be calculated. Internal energy as well as heat capacitance will also be analyzed. Low-temperature behavior of these quantities will be compared to the corresponding ones of bulk-structures. It was shown that heat capacitances of nano-layered structures in low-temperature region were higher than the same quantities of the corresponding bulk sample. In the middle and the highest temperature region, temperature behavior was inverse: heat capacitance of layered structures was lower than of the corresponding bulk ones. The consequences were discussed with relation to the better superconductive properties of nanomaterials.