Polyoxymethylene diethyl ethers (PODEEn) are oxygenated fuel additives with high performance due to their advantageous fuel properties. PODEEn can alleviate carbon debt as the production can utilize bioethanol and biomass syngas. Heterogeneous solid acid catalysts are desirable for an efficient PODEEn synthesis. In this study, well-defined sulfonated phthalocyanine-containing polymers were prepared, and the physicochemical properties were analyzed, exhibiting a 2D π-π stacking structure with crystalline-amorphous mixed phases. Owing to the tuning defects of the COF framework by mixing polymerization, the accessibility of the network and the capacity of strong acid were improved for the polymeric catalyst, showing an excellent activity with trioxane (TOX) conversion of 89% and PODEE2-8 selectivity of 87% at 80 °C under atmospheric pressure.