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Heterojunctions and multi-gated structures facilitate the fabrication of high-performance and multifunctional transistors. Here, a WSe2/MoS2 heterojunction structure transistor with a back gate and two top gates is proposed. The back gate controls the carrier transport of the entire heterojunction channel, and the top gates independently control the carrier transports of MoS2 or WSe2 channels. The rectification direction of the heterojunction device could be reversed, and the rectification ratio could be modulated from 10−4 to 104 by changing the back-gate voltage. In addition, an evident negative-differential transconductance phenomenon with a current peak and a current valley are observed in the back-gate transfer characteristic curve, which results from the different control ability of the same gate voltage to the Fermi levels in MoS2 and WSe2. The current peak can be obviously modulated and eliminated by the MoS2 top gate, while the WSe2 top gate can control the position of the current valley from −8 to +12 V, which clearly supports the heterostructure energy band model. Moreover, the diversity of output states under multi-gate modulation makes applications in logic circuits possible. These results demonstrate the potential of this approach for the development of next-generation electronic functional devices.