There are many risk sources on the segment floating transportation route of inland river immersed tunnel. The risk differences between segment floating transportation in sea and that in river are compared. The risks, including segment undocking, low water level points, segment crossing bridge with small span, segment turning area with high flow velocity and segment floating transportation in area with high flow velocity, are assessed and classified by risk matrix method. The risks of segment floating transportation are predicted and their countermeasures are summarized. The segment floating transportation for the first time is successful and can provide reference for followup segment floating transportation.