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The Flexible Job Shop Problem (FJSP) is a well-studied combinatorial optimization problem with extensive applications for manufacturing and production scheduling. It involves assigning jobs to various machines to optimize criteria, such as minimizing total completion time. Current learning-based methods in this domain often rely on localized feature extraction models, limiting their capacity to capture overarching dependencies spanning operations and machines. This paper introduces an innovative architecture that harnesses Mamba, a state-space model with linear computational complexity, to facilitate comprehensive sequence modeling tailored for FJSP. In contrast to prevalent graph-attention-based frameworks that are computationally intensive for FJSP, we show our model is more efficient. Specifically, the proposed model possesses an encoder and a decoder. The encoder incorporates a dual Mamba block to extract operation and machine features separately. Additionally, we introduce an efficient cross-attention decoder to learn interactive embeddings of operations and machines. Our experimental results demonstrate that our method achieves faster solving speed and surpasses the performance of state-of-the-art learning-based methods for FJSP across various benchmarks.