Nuclear power, as a low-carbon energy source, provides the steady and reliable electricity. In this power source, safe operation plays a significant role from the point of view of design and economic cost. While nuclear power plants are designed to be safe in their operation and safe in the event of any malfunction or accident, some accidents with considerable occurrence frequency should be considered to provide related safety system and operation. The malfunction of boron injection system is one of this accident affecting the chemical and neutronic characteristics of cooling fluid. The aim of this study is the simulation and analysis of the boron dilution accident as one of Design Basis Accident, by considering the heterogeneous distribution of boron. For this purpose, CFD methods were used for exact evaluation of the boron distribution in each fuel assembly. Also, cross-section correction module and core calculation module are respectively developed by a cell calculation code and nodal expansion method. These modules are employed to apply absorber effects including boron and control banks and calculate 3D relative power. The results reveal the effect of heterogeneous distribution of boron in reactor pressure vessel and non-uniform chemical characteristics of coolant across fuel channels.