Abstract Dense hydrous magnesium silicates (DHMSs) with large water contents and wide stability fields are a potential H2O reservoir in the deep Earth. Al-bearing superhydrous phase B (shy-B) with a wider stability field than the Al-free counterpart can play an important role in understanding H2O transport in the Earth’s transition zone and topmost lower mantle. In this study, a nominally Al-free and two different Al-bearing shy-B samples with 0.47(2) and 1.35(4) Al atoms per formula unit (pfu), were synthesized using a rotating multi-anvil press. Their single-crystal structures were investigated by X-ray diffraction (XRD) complemented by Raman spectroscopy and Fourier-transform infrared spectroscopy (FTIR). Single-crystal XRD shows that the cell parameters decrease with increasing Al-content. By combining X-ray diffraction and spectroscopy results, we conclude that the Al-poor shy-B crystallizes in the Pnn2 space group with hydrogen in two different general positions. Based on the results of the single-crystal X-ray diffraction refinements combined with FTIR spectroscopy, three substitutions mechanisms are proposed: 2Al3+ = Mg2+ + Si4+; Mg2+ = ☐Mg2+ + 2H+ (☐Mg2+ means vacancy in Mg site); Si4+ = Al3+ + H+. Thus, in addition to the two general H positions, hydrogen is incorporated into the hydrous mineral via point defects. The elastic stiffness coefficients were measured for the Al-shy-B with 1.35 pfu Al by Brillouin scattering (BS). Al-bearing shy-B shows lower C11, higher C22, and similar C33 when compared to Al-free shy-B. The elastic anisotropy of Al-bearing shy-B is also higher than that of the Al-free composition. Such different elastic properties are due to the effect of lattice contraction as a whole and the specific chemical substitution mechanism that affect bonds strength. Al-bearing shy-B with lower velocity, higher anisotropy, and wider thermodynamic stability can help understand the low-velocity zone and the high-anisotropy region in the subducted slab located in Tonga.