A type-2 hierarchical fuzzy system (T2HFS) is presented for the high-dimensional data-based modeling with uncertainties. Type-2 fuzzy logic system (T2FLS) is a powerful tool to handle uncertainties in complex processes. However, the operation of type-reduction has greatly increased the computational burden of T2FLSs. By integrating the T2FLS with hierarchical structure, a systematic design methodology of T2HFS is proposed to avoid the rule explosion and to simplify the computation complexity. The design methodology has included several procedures to establish the T2HFS. Firstly, the PCA-based method is developed to capture the prominent component from training data, and to determine the hierarchical structure of T2HFS. Furthermore, a novel clustering method is proposed to design the basic type-2 fuzzy logic unit (T2FLU) in uncertain environments. Finally, a hybrid-learning method is presented to fine-tune the parameters for the global optimization where the statistical and deterministic optimization methods are developed for the nominal and auxiliary performance, respectively. Simulation results have shown that the proposed T2HFS is very effective for the high-dimensional data-based modeling and control in uncertain environment.