Trivalent lanthanide ions (Ln3+) have been used as active centers for fluorescence mainly in inorganic crystalline or glassy solids. Ln3+-containing systems allow easier thermal emission with narrower energy gaps under near-infrared light excitation because the Ln3+ electron-phonon interaction is a weak coupling. The multiphonon relaxation theory helps to quantitatively deal with heat release in the ionic inorganic solids. Recent advances in producing Ln3+-doped nanocrystals, however, are demanding alternative design concepts for Ln3+-based nanomaterials that exhibit luminescence in organic or organic/inorganic hybrid systems. In this paper we discuss the approach for dealing with the effect of organic molecules that surround the Ln3+-doped nanocrystals with the quantitative treatment of electron-phonon coupling. We conclude that this effect is substantially explicable by the chemical polarity of surrounding molecules. This paper reviews applications using thermal absorption and emission including laser cooling and thermometry, as well as biophotonic applications involving the thermal interaction of the Ln3+ such as nanothermometry and photothermal therapy.