This invention is directed to a flexible solar cell photovoltaic module with high light transmittance based on modified substrate, which belongs to the field of thin-film solar cell technology. The objective of the present invention to provide a technical solution for a transparent flexible solar cell module and its fabrication method. Technical features include using a stainless steel template to mold a modified polyimide PI substrate (the PI substrate). The PI substrate has light-passing through-holes, including draining holes and convergence holes, through and distributed on the PI substrate, a conductive film layer, and various stacked photoelectric conversion film layers. The creativeness of the present invention is obvious, such as reducing the short circuit and current leakage due to crystallization of the photoelectric layer interface caused by a subsequent process of laser etching the conductive film layer, reducing the composition on the surface of the solar cell, reducing steps of the fabrication process, and lowering the production cost. Further, the present invention significantly increases the conversion efficiency and load capacity of the solar cell and the quality-cost ratio. The transparent flexible solar cell photovoltaic module also has a broad range of applications.