Abstract 2D material‐based heterostructures are constructed by stacking or spicing individual 2D layers to create an interface between them, which have exotic properties. Here, a new strategy for the in situ growth of large numbers of 2D heterostructures on the centimeter‐scale substrate is developed. In the method, large numbers of 2D MoS 2 , MoO 2 , or their heterostructures of MoO 2 /MoS 2 are controllably grown in the same setup by simply tuning the gap distance between metal precursor and growth substrate, which changes the concentration of metal precursors feed. A lateral force microscope is used first to identify the locations of each material in the heterostructures, which have MoO 2 on the top of MoS 2 . Noteworthy, the creation of a clean interface between atomic thin MoO 2 (metallic) and MoS 2 (semiconducting) results in a different electronic structure compared with pure MoO 2 and MoS 2 . Theoretical calculations show that the charge redistribution at such an interface results in an improved HER performance on the MoO 2 /MoS 2 heterostructures, showing an overpotential of 60 mV at 10 mA cm −2 and a Tafel slope of 47 mV dec −1 . This work reports a new strategy for the in situ growth of heterostructures on large‐scale substrates and provides platforms to exploit their applications.