In order to meet the new challenges on the energy and environment, a new conceptual design of nuclear heating reactor (HAPPY200) is developed. HAPPY200 is a two-loop low pressure water reactor with low thermal parameters and passive safety systems. The outlet temperature is 120 °C, the inlet temperature is 80 °C, and the operating pressure is 0.6MPa. In this study, the thermal performance problems of big and small fuel assemblies are discussed for HAPPY200. Under the same total power condition, the small assembly core is better considering thermal performance. And under the same average rod power condition, the small assembly core condition 2 is better considering thermal performance. Considering maturity and economic factor comprehensively, the big assembly core is chosen in the near term.