We compute the two-loop master integrals for non-leptonic heavy-to-heavy decays analytically in a recently-proposed canonical basis. For this genuine two-loop, two-scale problem we first derive a basis for the master integrals that disentangles the kinematics from the space-time dimension in the differential equations, and subsequently solve the latter in terms of iterated integrals up to weight four. The solution constitutes another valuable example of the finding of a canonical basis for two-loop master integrals that have two different internal masses, and assumes a form that is ideally suited for a subsequent convolution with the light-cone distribution amplitude in the framework of QCD factorisation.