In the past decade, great progresses have been made in WiFi-based device-free localization (DFL). However, some challenging issues still hinder the large-scale implementation of DFL techniques, mainly including fingerprint vanishing and environmental dynamics. In order to enhance the localization performance in cluttered environments, in this article, a modified hierarchical framework for DFL is designed, which consists of several functional modules. Specifically, the collected data are first divided into several subsets in the spatiotemporal separation module. Next, the raw data are mapped to another feature space to mitigate the effects of fingerprint vanishing with the help of a deep neural network. In the distributed modeling module, local DFL models are built to separately represent the subsets. Additionally, probability distributions of local DFL models are calculated to estimate and control the effects of the noise. Finally, a global DFL model is built by integrating all the local DFL models with the embedding of the probability distribution information of those local DFL models. In this manner, the localization performance in cluttered environments could be significantly enhanced by the proposed hierarchical framework. Comprehensive experiments in several indoor environments demonstrate the robustness and generalization performance of the proposed hierarchical framework.