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Abstract The direct detection of gravitational waves offers a powerful tool to explore the nature of gravity and the structure of space-time. This paper focuses on the capabilities of space-based gravitational wave detectors in testing space-time non-commutativity. Our findings indicate that TianQin has the potential to impose constraints on the non-commutative scale at a sub-Planckian level using massive black hole binaries. Additionally, we have developed a pipeline tailored to this specific topic.