The control of single atoms offers fundamental insight into understanding the charge transport through single clusters, and the atomic precision of the clusters provides the opportunity to manipulate the charge transport even at the single-atom level. Herein, we designed and investigated the electrical conductance and thermopower of Anderson-type polyoxometalate (POM) clusters with single-atom variation using the scanning tunneling microscopy break-junction (STM-BJ) technique. Our results show the electrical conductance of single clusters can be changed by an order of magnitude by substituting different center-metal atoms, and the electrical conductance of clusters shows different bias-dependence. Furthermore, the Seebeck coefficients of the POM clusters also can be significantly changed by the center-metal atoms. The non-equilibrium quantum transport calculations reveal that the electrostatic potential profile is non-uniformly dependent on the center-metal atoms. This leads to gating of electrical conductance by bias voltage. This supports the tuning of thermopower and bias dependent transmission spectra. This work provides the fundamental understanding of single-atom control of charge transport in POM single-cluster junctions.