A new open-framework germanate, denoted as GeO-JU90, was prepared by the hydrothermal synthesis method using 1,5-bis(methylpyrrolidinium)pentane dihydroxide as the organic structure-directing agent (SDA). The structure of GeO-JU90 was determined from synchrotron X-ray powder diffraction (XRPD) data using the charge-flipping algorithm. It revealed a complicated framework structure containing 11 Ge atoms in the asymmetric unit. The framework is built of 7-connected Ge7 clusters and additional tetrahedral GeO3(OH) units forming a new three-dimensional interrupted framework with interesting 12 × 12 × 11-ring intersecting channels. The Ge K-edge extended X-ray absorption fine structure (EXAFS) analysis was performed to provide the local structural information around Ge atoms, giving rise to a first-shell contribution from about 4.2(2) O atoms at the average distance of 1.750(8) Å. The guest species in the channels were subsequently determined by the simulated annealing method from XRPD data combining with other characterization techniques, e.g., (13)C NMR spectroscopy, infrared spectroscopy (FTIR), compositional analyses, and thermogravimetric analysis (TGA). Crystallographic data |(C15N2H32)(NH4)|[Ge11O21.5(OH)4], orthorhombic Ama2 (No. 40), a = 37.82959 Å, b = 15.24373 Å, c = 12.83659 Å, and Z = 8.