A multi-dimensional thermal-hydraulic system analysis code, MARS 1.3.1, has been developed in order to have the realistic analysis capability of two-phase thermal-hydraulic transients for pressurized water reactor (PWR) plants. As the backbones for the MARS code, the RELAP5/MOD3.2.1.2 and COBRA-TF codes were adopted in order to take advantages of the very general, versatile features of RELAP5 and the realistic three-dimensional hydrodynamic module of COBRA-TF. In the MARS code, all the functional modules of the two codes were unified into a single code first. Then, the source codes were converted into the standard Fortran 90, and then they were restructured using a modular data structure based on "derived type variables" and a new "dynamic memory allocation" scheme. In addition, the Windows features were implemented to improve user friendliness. This paper presents the developmental work of the MARS version 1.3.1 including the hydrodynamic model unification, the heat structure coupling, the code restructuring and modernization, and their verifications.their verifications.