The invention discloses a material transport system compatible with multiple process silicon wafers. The material transport system comprises a silicon wafer storage unit, a manipulator unit and a pre-alignment unit, wherein the pre-alignment unit is used for carrying out centering orientation on the silicon wafers and comprises a linear module, a lifting module, a rotating module and a centering table; the linear module and the centering table are fixed to a bottom plate; the lifting module is fixed to the linear module; the linear module drives the lifting module to carry out horizontal motion; a rotating shaft of the rotating module is fixed to the lifting module; the lifting module drives the rotating module to carry out vertical motion; the rotating module can drive the silicon wafers thereon to carry out rotary motion; the rotating module is arranged on the centering table in a penetrating manner; when the rotating module is located at the highest position, the upper surface of the rotating module is higher than that of the centering table; when the rotating module is located at the lowest position, the upper surface of the rotating module is lower than the lower surface of the centering table.