A series of zeolites with different topology structures, including SAPO-34, SUZ-4, ZSM-5, USY, MOR, and beta, were used to synthesize polyoxymethylene dimethyl ethers (PODEn) from dimethoxymethane (DMM) and trioxymethylene (TOM). The influence of acidic properties and channel systems were studied by activity evaluation, characterization, and theoretical calculation. The results confirmed that pore mouth diameter larger than a TOM molecule was an essential prerequisite for the synthesis of PODEn over zeolites, and the synergistic effect between medium-strong Brønsted acid sites (Brønsted MAS) and the maximal space of zeolites available determined the catalytic performance of all studied zeolites. DMM and TOM were firstly decomposed into methoxymethoxy groups (MMZ) and monomer CH2O over Brønsted MAS. Subsequently, the steric constraint of the maximum included sphere, with an appropriate size in zeolite channels, can promote the combination of CH2O and MMZ to form transition species ZO(CH2O)nCH3, which reacted with the methyl-end group to form PODEn over Brønsted MAS. Moreover, the reaction temperature showed different effects on the product selectivity and distribution, which also mainly depends on the size of the maximum space available in zeolite channels.