In collinear factorization, light-cone distribution amplitudes (LCDAs) are key ingredients to calculate the production rate of a hadron in high energy exclusive processes. For a doubly-heavy meson system (such as B c , J/ψ, Υ etc), the LCDAs contain perturbative scales that can be integrated out and then are re-factorized into products of perturbatively calculable distribution parts and non-relativistic QCD matrix elements. In this re-factorization scheme, the LCDAs are known at next-to-leading order in the strong coupling constant α s and at leading order in the velocity expansion. In this work, we calculate the O(v 2 ) corrections to twist-2 LCDAs of S-wave B c mesons. These results are applicable to heavy quarkonia like η c,b , J/ψ and Υ by setting m b = m c . We apply these relativistically corrected LCDAs to study their inverse moments and a few Gegenbauer moments which are important for phenomenological study. We point out that the relativistic corrections are sizable, and comparable with the next-to-leading order radiative corrections. These results for LCDAs are useful in future theoretical analyses of the productions of heavy quarkonia and B c mesons.