If each phase has an identical crystal structure and small misfit in the lattice parameters in a binary-phase crystalline system, coherent phase boundaries usually form during separation. Although there have been numerous studies on the effect of coherency elastic energy, no attempt has been made to demonstrate how the phase-separation behaviour varies when multiple interfaces meet at a junction. Here we show that a comprehensively different phase-separation morphology is induced, to release the high coherency strain confined to quadruple junctions. High-temperature in-situ transmission electron microscopy reveals that phase boundaries with a new crystallographic orientation emerge over twinned crystals to provide strain relaxation at quadruple junctions. The high coherency strain and the formation of different phase boundaries can be understood in terms of the force equilibrium between interface tensions at a junction point. Visualizing the quadruple points at atomic resolution, our observations emphasize the impact of multiple junctions on the morphology evolution during phase separation.