Polyoxymethylene dimethyl ethers (PODE) are excellent promising diesel oil additives or replacements because of the special structure without carbon-carbon bond. A novel solid dichlorodiphenylsilane-modified ZrO2--Al2O3 catalyst with both hydrophobic and hydrophilic sites exhibited good catalytic activity and desired product selectivity for the reaction of methanol and formaldehyde aqueous solution to PODE. A single type of active center (only hydrophobic center or hydrophilic center) did not perform well for the PODE synthesize reaction from methanol and formaldehyde because of the different hydrophobic properties of methanol, formaldehyde, methylal, and PODE. The experimental results confirmed that the hydrophobic sites and hydrophilic sites of the catalyst surface promote the synthesis of PODE and methylal, respectively. The enhancement of the hydrophobic property of the catalyst surface promotes the production of long chain PODE. Further study indicated that the product distribution can be controlled artificially by adjusting the content of hydrophobic agent, and the desired polymerization degree of PODE can be optimally synthesized by a modified catalyst (called HYB-26.9@ZrO2--Al2O3). Reaction temperature and pressure were also investigated for the PODE synthesis reaction with this modified catalyst, HYB-26.9@ZrO2--Al2O3. Low reaction temperature benefits the synthesis of long chain PODE because of the limit of reaction equilibrium. The stability of the catalyst was proven by a 240-hour running test.