The design of nuclear power units usually retains a certain design margin. By using the thermal system model of the secondary circuit of a nuclear power unit, factors affecting the output of the unit can be analyzed and optimized for operation, thereby effectively improving the economic benefits of the thermal cycle and tapping into the potential of the unit. It is also possible to optimize and analyze the design process, providing theoretical basis for reducing construction costs. This article uses PEPSE software as a modeling tool. The equipment calibration adopts the “dominant factor method”. The variable operating condition characteristic curve was calibrated. The accuracy of the thermal system model has been improved. Through the verification of design parameters, the data error is less than 0.32%, which should meet the needs of engineering applications. Based on engineering applications and scientific research needs, research has been conducted on the design margin of low-pressure heaters. The results indicate that using a thermal system model for equipment or system simulation analysis should be able to achieve optimization design margins and provide guidance for engineering design.