Efficient thermal management plays a significant role in a thermophotovoltaic system, especially in exploring the energy conversion characteristics of thermophotovoltaic cells (TPVC). If the cooling effect is insufficient, it is easy to cause temperature differences along the thickness direction of the cell. Meanwhile, temperature non-uniformity will cause electrical mismatch loss and reduce the reliability of cells. Therefore, a new design of a double-sided asymmetric cooling arrangement for testing the energy conversion performance of the TPVC at high-flux irradiation is proposed. This design consisted of a multi-channel water-cooling structure at the back (lower surface) of the TPVC, and the nitrogen is used to cool the TPVC radiation surface (upper surface). A three-dimensional structural computational model was created to examine the potential of the new design to lower cell temperature. According to the simulation results, compared with the conventional method, when the temperature of the radiation source is 2000 K, 2500 K, and 3000 K, the energy conversion efficiency has been improved by 7.23%, 17.97%, and 24.12%, respectively. Double-side cooling has a 30% higher uniformity at high-flux incident radiation than single-side cooling. Therefore, this new design model not only reduces the temperature difference between the upper and lower surfaces but also increases the temperature uniformity.