Phonons are the quantum mechanical descriptions of vibrational modes that manifest themselves in many physical properties of condensed matter systems. As the size of electronic devices continues to decrease below mean free paths of acoustic phonons, the engineering of phonon spectra at the nanoscale becomes an important topic. Phonon manipulation allows for active control and management of heat flow, enabling functions such as regulated heat transport. At the same time, phonon transmission, as a novel signal transmission method, holds great potential to revolutionize modern industry like microelectronics technology, and boasts wide-ranging applications. Unlike fermions such as electrons, polarity regulation is difficult to act on phonons as bosons, making the development of effective phonon modulation methods a daunting task. This work reviews the development of phonon engineering and strategies of phonon manipulation at different scales, reports the latest research progress of nanophononic devices such as thermal rectifiers, thermal transistors, thermal memories, and thermoelectric devices, and analyzes the phonon transport mechanisms involved. Lastly, we survey feasible perspectives and research directions of phonon engineering. Thermoelectric analogies, external field regulation, and acousto-optic co-optimization are expected to become future research hotspots.