Conventional internal combustion engine vehicles generally have less than a 30% of fuel efficiency, and the most wasted energy is dissipated in the form of heat energy. The excessive heat dissipation is a primary reason of poor fuel efficiency, but reclamation of the heat energy has not been a main focus of vehicle design. Thanks to thermoelectric generators (TEGs), wasted heat energy can be directly converted to electric energy. All the heat exchangers, including vehicle radiators, gradually cool down the coolant or gas from the inlet to outlet. TEG modules are commonly mounted throughout the heat exchanger to fulfill the required power density and voltage. Each TEG module has a different hot-side temperature by the mounting location (distance from the inlet) and thus different maximum power point (MPP) voltage and current. Nevertheless, TEG modules are commonly connected in series and parallel, where both the ends are connected to a single power converter. As a result, the whole TEG module array exhibits a significant efficiency degradation even if the power converter has the MPP tracking capability. Although material and device researchers have been putting a lot of effort in enhancing TEG efficiency, such system-level issue has not been deeply investigated. This paper proposes a cross-layer, system-level solution to enhance TEG array efficiency introducing online reconfiguration of TEG modules. The proposed method is useful for any sort of TEG arrays to reclaim wasted heat energy, because heat exchangers generally have different inlet and outlet temperature values. This paper also introduces a complete design and implementation showcase of a reconfigurable TEG module building block. Experimental results show up to a 34% enhancement using the proposed method compared with a fixed array structure, which is a common practice.