Abstract: In physical analysis of the cobalt adjuster rods design change for Qinshan Phase Ⅲ, the incremental cross section used in RFSP-IST code for the cobalt adjuster rod was calculated by DRAGON, whose methodology was not exactly the same as the MULTICELL used for Qinshan Phase Ⅲ RFSAR (2007), hence it was necessary to do the uncertainty analysis for RFSP-IST code flux calculation after cobalt adjuster rod replacement. Based on the historical data from Unit 1 and Unit 2 of Qinshan Phase Ⅲ, the uncertainty analysis of RFSP-IST code flux calculation was done with 95/95 upper tolerance limit method. Numerical results show that the cobalt adjuster rod design change and different incremental cross section calculation codes do not impact the uncertainty of RFSP-IST code flux calculation.