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Existing approaches typically approximate such features within continuous function spaces, often requiring increased model capacity and high-resolution data. In this work, we propose Cut-DeepONet, a two-stage training framework that explicitly models discontinuities while reducing learning complexity. Our approach reformulates the problem via a lifting strategy, partitioning the domain into smooth subregions while representing discontinuities as boundaries in a higher-dimensional space. This separation aligns the operator learning task with the inductive bias of neural networks and avoids directly approximating discontinuities. 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