Depositing amorphous silicon doped with different elements on flexible substrates offers a large potential for the roll-to-roll processes lowering the manufacturing cost of solar cells. Unique magnetron sputtering method was adopted to deposit B-doped amorphous silicon thin film on flexible PET substrate instead of solid substrate materials like glass, metal and silicon. Effects of different substrates were investigated, as well as the processing parameters including sputtering power and working pressure. The structure and performance of the samples were characterized with SEM, XRD, surface profile meter and UV-spectrophotometer. The comparison between PET and glass shows that the alternative of PET substrate significantly improved the deposition rate. Optimal results were obtained as pressure of 0.2 Pa and RF power of 120 W, which showed the lowest transmittance as well as a minimum optical band gap, both are of great significance to photovoltaic conversion. Theoretical justification and experimental data including the feasible magnetron sputtering way, PET flexible substrate and optimized process parameters to the mass production of cheap and high performance heterojunction thin film solar cells were achieved.