Abstract. In JAEA, mode conversion by corrugated waveguide system which is ITER relevant TL system was studied. To evaluate the alignment method for TL assembly, the mode content of middle section of TL was measured while assembly of the TL test stand. Then 5% of LP01 mode purity degradation was found in the long straight section though it was just assembly of 2m straight WGs. Indeed, the mode conversion calculation showed that 5% of mode conversion may occur when the straight section causes 1.0 mm of periodic deflection. To minimize the deflection, the alignment method with adjustment of both position and angle of the WG piece utilizing the laser beam reflection was applied for the TL re-assembling. The mode purity in the same section was improved and mode purity degradation was less than 1%. Finally 93% of LP01 mode purity was achieved at the end of long TL. Next the effect of mode purity by high-power long-pulse operation in TL was studied. Since the TL components are heated during the high-power RF operation, the TL causes deformation due to thermal expansion and deformed TL section induces significant mode conversion loss. The 170GHz gyrotron provided high-power (400kW) and long pulse (500sec) into TL and the beam profile at TL end was measured both before and after the long pulse operation. The mode purity at TL end was 91% before the long pulse and it decreased to 84% after the pulse. The temperature distribution and displacement of TL components were also measured. The measured displacement shows that the vertical sections became S-bend structures and mode conversion loss was estimated. The estimated total mode conversion loss in deformed long TL system was 8%. The estimated value showed good agreement with measurement of mode purity.