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Polygon-based object representations efficiently model object boundaries but are limited by high optimization complexity, which hinders their adoption compared to more flexible pixel-based methods. In this paper, we introduce a novel vertex regression loss grounded in Fourier elliptic descriptors, which removes the need for rasterization or heuristic approximations and resolves ambiguities in boundary point assignment through frequency-domain matching.To advance polygon-based instance segmentation, we further propose EFDTR (\textbf{E}lliptical \textbf{F}ourier \textbf{D}escriptor \textbf{Tr}ansformer), an end-to-end learnable framework that leverages the expressiveness of Fourier-based representations. The model achieves precise contour predictions through a two-stage approach: the first stage predicts elliptical Fourier descriptors for global contour modeling, while the second stage refines contours for fine-grained accuracy. Experimental results on the COCO dataset show that EFDTR outperforms existing polygon-based methods, offering a promising alternative to pixel-based approaches. Code is available at \url{https://github.com/chrisclear3/EFDTR}.