The rare earth manganite BaLn2Mn2O7 (Ln=rare earth element) has a Sr3Ti2O7-type layered perovskite structure with double-block oxygen octahedra belonging to the Ruddlesden-Popper-type homologous series AO(ABO3)2. In Pr-manganite, a novel phase transition was first observed in situ at 1040 K by a thermal transmission electron microscope. At 1040 K, reflections began to split along the c-direction in the selected area diffraction pattern. This indicates that a new phase appears in the original phase matrix; the c length of the new phase is 1.5% longer than that of the original phase. After about 5 min, the original phase disappears. No change in the crystal symmetry (space group I4/mmm) is observed above 1040 K.