Phosphotungstic acid (HPW) was added to mesoporous silica (MS) to form catalysts by two distinct methods, i.e., a direct-synthesis method and an impregnation method. The catalysts were evaluated in the synthesis of soybean oil-based polyols. The epoxidized soybean oil (EBSO) was successfully converted to polyols using methanol as the ring open reagent. The results indicated that the optimal loading of the HPW is approximately 25 wt%. The two different catalysts showed distinct catalytic behaviors. We found that the impregnated 25%HPW/MS presented better conversion of polyols, whereas the direct-synthesized 25%HPW-MS showed enhanced reusability and stability. Moreover, the 25%HPW-MS had advantages of reducing side reactions and suppressing the formation of oligomers, as well as higher product selectivity. Accordingly, the methods demonstrated a promising prospect in heterogeneous catalysis for soybean oil-based polyols conversion.