Understanding the underlying physics of interactions among various quasi‐particles is a fundamental issue for the application of spintronics and photonics. Here the observation of a coupling between the small polarons in the nanoscale ultrathin La0.7Sr0.3MnO3 (LSMO) films and the acoustic phonons in the SrTiO3 (STO) substrate using ultrafast pump–probe spectroscopy has been reported. According to the temperature‐ and wavelength‐dependent measurements, the amplitudes of the acoustic phonons are suppressed by tuning the small polarons absorption. This shows a coupled relationship between the acoustic phonons and the small polarons. At the probe photon energy of 1.55 eV where the polaron absorption is dominant, the acoustic phonons become unobservable. Furthermore, by performing the pump fluence dependent measurements on the LSMO films with different thicknesses, smaller acoustic phonon amplitudes are found in the thinner film with stronger small polaron binding energy. Such a coupled nature can be utilized to manipulate the small polarons using the acoustic phonons or vice versa, which is of great importance in device applications of colossal magnetoresistance materials.