We investigate the nonlinear Rosen-Zener transition in two-mode systems. A non-trivial collective behavior, in which all the atoms tend to stay at only one of the modes, emerges with the appearance of nonlinear interaction under the adiabatic approximation. The application of an external field can transfer the atoms from one mode to the other completely. Such phenomena can be fully understood with the help of the phase diagram. We expect the predicted effect will be detected in current BEC experiments.