This study numerically investigates the formation of high-velocity molecular clouds (HVMCs) in the Galactic Center (GC) based on the X-ray emission analysis. We employ three-dimensional magnetohydrodynamic simulations to explore the propagation and acceleration of HVMCs with starburst-driven winds, considering vertical, horizontal, and no magnetic field scenarios. Our results reveal that the envelope gas (with a typical T ∼ 108 K and density ∼10−2 cm−3) of molecular clouds (MCs) as a result of the shock interaction is responsible for X-ray emission. Additionally, some clear boundary exists between the interstellar medium (ISM), envelope gas and MCs, and the envelope gas protects the MCs in the heated environment of the shock wave. In theory, it is challenging to distinguish between the envelope gas, MCs and ISM in terms of X-ray emission. Our simulations suggest that the envelope gas has a significant impact on the survival and emission characteristics of MCs, providing insights into the complex interactions from the supernova feedback mechanisms in the GC.