Ba2M(B3O6)2 (M = Mg, Ca and Ba) are potential stimulated Raman scattering (SRS) crystals. Their Raman spectral peak positions that determine the SRS laser wavelengths are influenced by the M cations. When M is replaced in the order of Mg, Ca and Ba, all internally vibrational peaks red-shift except the peak below 600 cm−1. First-principles method was used to interpret the M cation effect. The calculated results show that the B–O bond populations decrease with the increase of the alkali-earth cation (Ba and M) populations in the order of Ba2Mg(B3O6)2, Ba2Ca(B3O6)2 and Ba2Ba(B3O6)2 (α-BBO, high-temperature phase BaB2O4 crystal), which weakens the B–O bonds and red-shifts the peaks arising from the internal modes. On the basis of the results, four important Raman vibrational peaks were discussed. The abnormal blue-shift of the peak located below 600 cm−1 is attributed to the Davydov splitting that originates from the interaction between two adjacent B3O6 rings. The splitting energies (Δ) of the Ba2Mg(B3O6)2, Ba2Ca(B3O6)2 and α-BBO crystals are 50 cm−1, 38 cm−1 and 25 cm−1, respectively.