The effect of decoherence on the phase transition of a Bose-Einstein condensate in a symmetric double-well potential is determined by the mean atom number difference. It still has two phases, the tunneling phase and the self-trapping phase, even under decoherence. The density matrix and the operator fidelity also show very different behaviors in the two phases. This suggests that operator fidelity can be used to characterize the phase transition of this Bose-Einstein condensate model, even under decoherence.