This paper targets at the state-of-art hybrid energy storage systems (HESSs) with a networked charge transfer interconnect and solves a node placement problem in the HESS, where a node refers to a storage bank, a power source, or a load device, with its distributed power converter. In particular, the node placement problem is formulated as how to place the nodes in a HESS such that the optimal total charge transfer efficiency is achieved, with accurate modelings of all kinds of different components in the HESS. The methodology of FPGA placement problem is adopted to solve the node placement in HESS by properly defining a cost function that strongly relates the charge transfer efficiency to the node placement, properties of HESS components, as well as applications of the HESS. An algorithm that combines a quadratic programming method to generate an initial placement and a simulated annealing method to converge to the optimal placement result is presented in this paper. Experimental results demonstrate the efficacy of the placement algorithm and improvements in the charge transfer efficiency for various problem setups and scales.