Zeolites with large cavities that are accessible via wide pore windows are desirable but very rare. They have been dominantly used as catalysts in industry. Here we report a novel porous germanosilicate SCM-25, the zeolite structure containing ordered meso-cavities (29.9 × 7.6 × 6.0 ų) interconnected by 10- and 12-ring channels. SCM-25 was synthesized as nanosized crystals by using a simple organic structure-directing agent (OSDA). Three-dimensional (3D) electron diffraction shows that SCM-25 crystallizes in the orthorhombic space group Cmmm with a = 14.62 Å, b = 51.82 Å, c = 13.11 Å, which is one of the zeolites with the largest unit cell dimensions. We demonstrate that 3D electron diffraction is a powerful technique for determining the complex structure of SCM-25, including the disorders and distributions of framework atoms silicon and germanium. SCM-25 has a high surface area (510 m²/g) and high thermal stability (700 °C). Furthermore, we propose a potential postsynthetic strategy for the preparation of zeolites with ordered meso-cavities by applying the ADOR (assembly–disassembly–organization–reassembly) approach.