Adoption of higher burn-up core can be considered as one of effective methods to enhance economic competitiveness for the commercialization of sodium-cooled fast reactors and it becomes possible with evaluating and confirming structural integrity of fuel assemblies under high bum-up conditions. A numerical simulation system, which consists of a deformation analysis program and three kinds of thermal-hydraulics analysis programs, is being developed in Japan Atomic Energy Agency (JAEA) in order to offer methodologies to clarify thermal-hydraulic phenomena in fuel assemblies under various operating conditions. In this paper, an analysis method of thermal-hydraulics in a wire-wrapped and deformed fuel pin bundle using two kinds of component programs of the numerical simulation system and its application to an irradiated fuel assembly analysis are described.