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By taking into account all the irreducible representations and their components in the electron-phonon interaction (EPI) as well as all the levels and the admixtures of basic wavefunctions within d(3) electronic configuration, the values of the parameters in the expressions of thermal shift (TS) from EPI for the ground level, R level and R line of SrTiO3:Mn4+ have been evaluated; the R-line TS and various contributions to it have been calculated in the low-temperature region. It is found that all the three terms of R-line TS from EPI relevant to the lattice vibration are red shifts. The Raman term is the largest, the neighbor-level term is the second, and the optical-branch term is very small over the range of T less than or equal to 80 K. The contribution to R-line TS from thermal expansion has been approximately neglected in this work. The very strong EPI relevant to its lattice vibration for SrTiO3:Mn4+ causes its R-Line TS to be an unusually large red-shift. Only by taking into account the strong softening of the low-frequency acoustic modes of the lattice vibration at low temperatures, can we successfully explain the variation of R-line TS of SrTiO3:Mn4+ with temperature.