We carried out in operando Mo K-edge X-ray absorption fine structure measurements on the rechargeable molecular cluster batteries (MCBs) of polyoxometalates (POMs), in which a Keggin-type POM, [PMo12O40](3-), is utilized as a cathode active material with a lithium metal anode. The POM-MCBs exhibit a large capacity of ca. 270 (A h)/kg in a voltage range between V = 4.0 V and V = 1.5 V. X-ray absorption near-edge structure analyses demonstrate that all 12 Mo6+ ions in [PMo12O40](3-) are reduced to Mo4+ in the discharging process. This means the formation of a super-reduced state of the POM, namely, [PMo12O40](27-), which stores 24 electrons, and this electron number can explain the large capacity of the POM-MCBs. Furthermore, extended X-ray absorption fine structure analyses reveal the molecular structure of [PMo12O44](27-), which is slightly reduced in size compared to the original [PMo12O40](3-) and involves Mo4+ metal-metal-bonded triangles. Density functional theory calculations suggest that these triangles are formed because of the large number of additional electrons in the super-reduced state.