The phenomenon of thermal quenching of luminescence can significantly compromise the efficiency of luminescent materials, a process accompanied by the generation of substantial phonon populations. While plenty of models for elucidating this behavior have been proposed, the crucial role of phonon transport has largely been neglected, particularly in the enigmatic incommensurate scheelite structure with good luminescence performance. In this study, we delve into the thermal quenching dynamics of the near-infrared emission in the incommensurately modulated CaGd2(MoO4)4:Yb/Er system. Our comprehensive investigation reveals distinct evolutionary patterns in electrical conductivity, luminescence intensity, thermal conductivity, and Raman scattering at varying temperature regimes. Notably, we have determined that thermally induced ion migration, occurring above ∼300 °C, serves as a pivotal trigger for the activation of all phonons and the enhancement of phonon-defect scattering within this incommensurate framework. This phenomenon not only diminishes the thermal conductivity but also accelerates the multiphonon relaxation of the Er3+ emission levels, culminating in a marked thermal quenching of luminescence. This work illuminates the thermal quenching mechanism of luminescence by focusing on phonon scattering dynamics, providing critical insights for the design of thermally robust near-infrared luminescent materials, which are essential for the advancement of optical amplification systems.