Layer-number-dependent performance of metal-semiconductor junctions (MSJs) with multilayered two-dimensional (2D) semiconductors has attracted increasing attention for their potential in ultrathin electronics and optoelectronics. However, the mechanism of the interaction and the resulting charge transfer/redistribution at the two kinds of interfaces in MSJ with multilayered 2D semiconductors, namely, the metal-semiconductor (M-S) and the semiconductor-semiconductor (S-S) interfaces, have not been well understood until now, although that is important for the overall Schottky barrier height and the energy-band-offset between different layers of the 2D semiconductors. Here, based on state-of-the-art density functional theory calculations, the mechanisms of bonding and asymmetric electron redistribution at the M-S and S-S interfaces of metal-bilayer MoS2 junctions are revealed. Multiple mechanisms collectively contribute to the electron redistribution at the two kinds of interfaces, and the dominant mechanism depends on both the dimensionality (2D vs 3D) and the work function of metal electrodes. For the M-S interface, the pushback effect and metal-induced gap states play a dominant role for MSJs with 3D metal, while the covalent-like quasi-bonding feature appears for MSJs with medium-work-function 2D metals, and charge transfer plays a main role for MSJs with 2D metals that have very large or small work functions. For the S-S interface, it inherits the electron-redistribution behavior of the M-S interface for MSJs with 2D metal, while opposite electron-redistribution appears in MSJs with 3D metal. These mechanisms provide general insights and new concepts to better understand and use MSJs with multilayered 2D semiconductors.