The direct whole-core calculations can provide accurate results and insights to the physics phenomena of the reactor. It can also capture the local effects of temperature and density fields on fuel depletion. However, the computational cost of the direct whole-core calculations is expensive. To compromise between computational cost and accuracy, the DDC-3D code system has been developed to perform neutronics and thermal-hydraulics coupling analysis. The DDC-3D code system couples the open-source codes DRAGON & DONJON based on two-step method and subchannel code COBRA-EN. The Picard iteration method is applied to ensure the stability of numerical calculation. Then the BEAVRS benchmark is used to validate the computational capabilities of DDC-3D code system. The critical boron concentrations, control rod worths and fission rate distributions are calculated in HZP condition. The results show a good agreement with measured data. The results demonstrate that the two-step method is applicable and valid for multiphysics simulations. For the result of HFP condition for cycle 1, the results also agree well with measured data, including the trend of the critical boron concentrations and power distributions throughout the cycle 1. Although the detailed thermal–hydraulic experimental values are not available, the thermal-hydraulics analysis of the hot fuel assemblies indicates that the calculation results are reasonable. In general, the results demonstrate the feasibility and accuracy of DDC-3D code system for neutronics and thermal-hydraulics coupling calculations and life cycle simulation of PWRs.