Two novel vanadoborates were synthesized under hydrothermal conditions with different conformations (eclipsed and staggered) Li5[V6B20O39(OH)11]·8H2O 1 and (enH)2(enH2)2Cs2[V6B20O42(OH)8(H2O)0.5]·3H2O 2 (en = ethylenediamine) and analyzed by single crystal X-ray diffraction, powder X-ray diffraction (PXRD) analysis, two-dimensional infrared correlation spectroscopy (2D-IR COS) Characterization and density functional theory calculations. The cluster anion of both compounds is [V6B20O50]16−, which is a sandwich structure composed of a V6 ring and two [B10O16] triangles. In compound 2, the two [B10O16] triangles of the [V6B20O50] 16−cluster anion are staggered by 60 degrees, forming an isomer configurationally different from compound 1. The similarities and differences between the 2D-IR COS spectra of the two compounds are explained from the structural point of view. Theoretical calculation shows that two staggered cluster anions have similar in energies and thus should be able to coexist. This study not only fills the gap in the study of the isomer of vanadoborates, but also makes an outstanding contribution to the study of the self-assembly mechanism of polyoxometalates.