We investigate many-body quantum fluctuation effects of Rosen-Zener transition of Bose-Einstein condensate (BEC) in a symmetric double-well potential through the relation between the average population imbalance of the final state (APIFS) and scanning period. In the linear case, we deduce the analytical expression of the APIFS which has the same behavior as in the mean-field level. We also employ numerical calculation to demonstrate it. In the nonlinear case, numerical results show that the APIFS in the sudden limit also accords with that in the mean-field level whereas in the adiabatic limit the many-body result is quite different from that of the mean-field case: the behavior of APIFS with respect to scanning period is similar to sinusoidal rather than rectangular oscillation, besides the oscillation period increases with both the total number N and the nonlinear parameter c increasing.