Abstract A signal can be represented as the sum of the intrinsic mode functions via performing the empirical mode decomposition. For the discrete time signals, the lengths of the intrinsic mode functions are equal to the lengths of the input signals. As there is usually more than one intrinsic mode function, the total numbers of discrete points of all the intrinsic mode functions are usually more than the lengths of the input signals. In other words, the empirical mode decomposition is an oversampled representation. For some applications such as the compression application, the oversampled representation is not preferred. Therefore, this paper proposes an optimal adaptive nonuniform filter bank design approach for performing the decimations on the intrinsic mode functions. In particular, the passbands of the intrinsic mode functions are estimated based on an adaptive gradient algorithm. Then, the intrinsic mode functions are nonuniformly downsampled and upsampled with the sampling integers derived based on their estimated passbands. Next, a bank of filters is employed to reconstruct the original signal. Here, the passbands of the filters are also derived based on those of the intrinsic mode functions. After that, the nonuniform filter bank design problem is formulated as a semi-infinite programming problem such that the total ripple energies of all the filters are minimized subject to the specifications on the absolute maximum values of both the real part and the imaginary part of the reconstruction error. The semi-infinite programming problem is approximated by a semi-definite programming problem. Computer numerical simulation results show that our proposed system could achieve a very small reconstruction error at a very small oversampling ratio.