The most numerical investigations of the thermal-hydraulic phenomena following the loss of the residual heat removal capability during the mid-loop operation of the pressurized water reactor were performed according to simplifications and are not sufficiently accurate. To perform more accurate and more reliable predictions of thermal-hydraulic accidents in a nuclear power plant using computational fluid dynamics codes, a more detailed methodology is needed. Modelling results identified that thermal stratification and natural convection are observed. Temperatures of lower monitoring points remain low, while temperatures of upper monitoring points increase over time. The water in the heated region, in the upper unheated region and the pipe region was well mixed due to natural convection, meanwhile, there is no natural convection in the lower unheated region. Water temperature in the pipe region increased after a certain time delay due to circulation of flow induced by natural convection in the heated and upper unheated regions. The modelling results correspond to the experimental data. The developed computational fluid dynamics methodology could be applied for modelling of two-component single/two-phase natural convection and thermal stratification phenomena during the mid-loop operation of the pressurized water reactor or other nuclear and non-nuclear installations at similar conditions.