The event-related desynchronization/synchronization(ERD/ERS) time courses of lower and upper alpha band rhythms during hand motor imagery are investigated respectively by Fourier Sectral Entropy (FSE) in this paper. By analyzing one group of BCI competition data, it was found that FSE within upper alpha band displays a pronounced increase and decrease over contralateral and ipsilaterai brain areas respectively at the onset of hand motor imagery, which is corresponding to the antagonistic ERD/ERS patterns in previous studies. Different from the upper alpha activity pattern, FSE within lower alpha band displays a consistent increase over both two hemispheres hand representative areas. The preliminary results show that FSE could disclose the different behaviors of the upper and lower alpha band rhythms so that a new idea with the complexity measure is provided to characterize functional dissociation of lower and upper frequency alpha rhythms in relation to hand motor imagery.