In this study, the hydraulic channel routing model was constructed to analysis the effect of flood control with the operation of Chungju Dam for 2006 flood. Study area was divided with up- and downstream of Chungju Dam in the upper Han River of Paldang Dam. The model was calibrated and verified for the flood event of 1995-2008. The effects of flood control of Chungju Dam were compared with the simulation results without the dam, and the rising effects of stage in the main observation stations were analyzed by the variation of released dam discharge. Consequently, the operation of Chungju Dam for 2006 flood was performed properly, but the effects of flood control of Chungju Dam were so focused in downstream of the dam that institutional complement was demanded to reduce the flood damage in the upper region of the dam. The limit of decision rule of downstream stage in the backwater region of dam was analyzed to solve the problem, and the decision rule of downstream stage was proposed to consider the discontinuity between the backwater region of dam and the design flood of upper stream. The proposed rule will be used to design the reduction of flood damage in upper stream of dam and to apply the analysis of region for flood damage.