In this paper, we investigate the channel estimation problem for extremely large-scale multiple-input multiple-output (XL-MIMO) systems with a hybrid analog-digital architecture, implemented within a decentralized baseband processing (DBP) framework with a star topology. Existing centralized and fully decentralized channel estimation methods face limitations due to excessive computational complexity or degraded performance. To overcome these challenges, we propose a novel two-stage channel estimation scheme that integrates local sparse reconstruction with global fusion and refinement. Specifically, in the first stage, by exploiting the sparsity of channels in the angular-delay domain, the local reconstruction task is formulated as a sparse signal recovery problem. To solve it, we develop a graph neural networks-enhanced sparse Bayesian learning (SBL-GNNs) algorithm, which effectively captures dependencies among channel coefficients, significantly improving estimation accuracy. In the second stage, the local estimates from the local processing units (LPUs) are aligned into a global angular domain for fusion at the central processing unit (CPU). Based on the aggregated observations, the channel refinement is modeled as a Bayesian denoising problem. To efficiently solve it, we devise a variational message passing algorithm that incorporates a Markov chain-based hierarchical sparse prior, effectively leveraging both the sparsity and the correlations of the channels in the global angular-delay domain. Simulation results validate the effectiveness and superiority of the proposed SBL-GNNs algorithm over existing methods, demonstrating improved estimation performance and reduced computational complexity.