Abstract: The structure of flow is very complex at Y shaped junction where there are multiform helix flows.This paper analyzes the effect of bed discordance (the ratio of bed discordant height between mainstream and tributary channel to the tailwater depth) on helix flow at Y shaped junction through the three-dimensional numerical simulation.The flow is dominated by two helical cells, usually back-to-back at Y shaped junction The bed discordance will decrease the intensity of helix flow at the side of mainstream channel and increase it at the side of tributary.When the intensity of helix flow is very strong at the side of tributary, the helix flow will be destroyed at the side of mainstream channel.