•We study crystal structure of higher manganese silicide (HMS) at high temperature.•The amount of secondary MnSi phase exceeds that of HMS phase above ∼1133 K.•Thermal expansion coefficients are almost the same as some typical metals.•(3+1)-Dimensional superspace approach reveals compositional change of HMS.•The Si composition γ decreases with temperature above 773 K. The (3+1)-dimensional crystal structure of a higher manganese silicide (MnSiγ) phase is revealed using in situ high temperature powder X-ray diffraction (XRD) above room temperature. The compound consists of two tetragonal subsystems of Mn and Si with an irrational c-axis ratio γ=cMn/cSi. The in situ XRD results show that the MnSiγ phase is stable, in a vacuum of ∼1 Pa, up to 1093 K and partially decomposes into the monosilicide (MnSi) phase with further increase in temperature. Refined a- and cMn-axis lengths increase linearly and the thermal expansion coefficients are comparable with those of typical metallic electrode materials. In contrast, cSi-axis length changes its increment against temperature at TBD ∼773 K. As a result, the temperature dependence of γ starts to decrease gradually above TBD, from 1.7387(1) (at 773 K) to 1.7244(1) (at 1173 K). This finding implies that the MnSiγ phase consecutively changes its irrational composition above TBD, a typical temperature where the silicides exhibit a maximum figure-of-merit. An increase in hole carrier concentration is expected according to the valence electron counting concept. Although the nearest Mn–Mn and Mn–Si distances increase monotonically with temperature, the nearest Si–Si distance much increases by ∼0.05 Åfrom 2.439(4) Åat 773 K to 2.493(7) Åat 1173 K. The latter increase is considered to be caused by the introduction of excited electron carriers into the anti-bonding orbital, due to the bipolar diffusion (BD).