In spatial databases, R-tree is one of the most widely used indexing structures and many variants have been proposed for its performance improvement. Among these variants, Hilbert R-tree is a representative method using Hilbert curve to process large amounts of data without high cost split techniques to construct the R-tree. This Hilbert R-tree, however, is hardly applicable to large-scale applications in practice mainly due to high pre-processing costs and slow bulk-load time. To overcome the limitations of Hilbert R-tree, we propose a novel approach for parallelizing Hilbert mapping and thus accelerating bulk-loading of Hilbert R-tree on GPU memory. Hilbert R-tree based on GPU improves bulk-loading performance by applying the inversed-cell method and exploiting parallelism for packing the R-tree structure. Our experimental results show that the proposed scheme is up to 45 times faster compared to the traditional CPU-based bulk-loading schemes.