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The stacking order plays a critical role in the electronic and optical properties of two-dimensional materials. It is however of great challenge to achieve large-size and homogeneous bilayer crystals with precisely controlled stacking orders. Here, we demonstrate an optimized chemical vapor deposition strategy to grow MoSe 2 bilayers with controlled AA or AB stacking sequences. Reverse gas flow effectively suppresses the random nucleation centers, leading to uniform growth of the second layer of MoSe 2 on the first monolayer. A customized temperature profile selectively activates the growth of the MoSe 2 bilayer with different stacking orders: the AA stacking MoSe 2 bilayer tends to form at 810 °C, and the AB stacking MoSe 2 bilayer prefers to grow at a higher temperature of 860 °C. A series of characterization methods confirm that MoSe 2 bilayers with different stacking orders exhibit distinct crystal structures and physical properties. Our results demonstrate a robust and effective route for the controllable synthesis of transition metal dichalcogenide bilayers, which will benefit the development of two-dimensional materials and van der Waals heterostructures.