A main steam line break (MSLB) test at the ATLAS facility was simulated using the best-estimate thermal-hydraulic system code, MARS-KS. This has been performed as an activity at the third domestic standard problem for code benchmark (DSP-03) that has been organized by Korea Atomic Energy Research Institute (KAERI). The results of the MSLB experiment and the MARS input data prepared for the previous DSP-02 using the ATLAS facility were provided to participants. The preliminary MSLB simulation using the base input data, however, showed unphysical results in the primary-to-secondary heat transfer. To resolve the problems, some improvements were implemented in the MARS input modelling. These include the use of fine meshes for the bottom region of the steam generator secondary side and proper thermal-hydraulics calculation options. Other input model improvements in the heat loss and the flow restrictor models were also made and the results were investigated in detail. From the results of simulations, the limitations and further improvement areas of the MARS code were identified.