At the Japan Atomic Energy Agency (JAEA), the simulation code “MUGTHES (MUlti Geometry simulation code for THErmal-hydraulic and Structure heat conduction analysis in boundary fitted coordinate)” has been developed to evaluate thermal striping phenomena that are caused by the turbulence mixing of fluids at different temperatures. In this paper, numerical schemes for thermal-hydraulic simulation employed in MUGTHES are described, including the LES model. A simple method to limit numerical oscillation is adopted in energy equation solutions. A new iterative method to solve the Poisson equation in the BFC system is developed for effective transient calculations. This method is based on the BiCGSTAB method and the SOR technique. As the code validation of MUGTHES, a numerical simulation in a T-junction piping system with the LES approach was conducted. Numerical results related to velocity and fluid temperature distributions were compared with existing water experimental data and the applicability of numerical schemes with the LES model in MUGTHES to the thermal striping phenomenon was confirmed.