In the design study of an advanced sodium-cooled fast reactor (Advanced-SFR) in Japan Atomic Energy Agency (JAEA), the use of a specific fuel assembly (FA) with an inner duct structure called FAIDUS has been investigated to enhance safety of Advanced-SFR against a core disruptive accident. Due to the asymmetric layout of fuel rods by the inner duct, it is necessary to estimate the temperature distribution to confirm feasibility of FAIDUS. In JAEA, an in-house subchannel analysis code named ASFRE has been developed as a FA design tool. For the typical FAs, the numerical results of ASFRE were validated by comparisons with experimental data. As for the FAIDUS, confirmation of validity of the numerical results by ASFRE was not enough because the reference data on the thermal hydraulics in FAIDUS have not been obtained by the mock-up experiment, yet. In this paper, therefore, the code-to-code comparisons with numerical results of ASFRE and those of an in-house CFD code named SPIRAL was conducted to make further discussion on applicability of ASFRE to the thermal-hydraulics analysis of FAIDUS. The applicability of ASFRE was indicated through the confirmation of the consistency of mechanism of the specific temperature and velocity distributions appearing around the inner duct between the numerical results by ASFRE and those by SPIRAL.