The synthesis of polyoxymethylene dimethyl ethers (PODEn), being green diesel fuel additives, from dimethoxymethane (DMM) and paraformaldehyde over three different cation resins, namely NKC-9, D001-CC, and D72, in a stirred-autoclave reactor was investigated. The pore size distribution and surface area were measured with nitrogen adsorption-desorption. NKC-9 had a larger exchange capacity, better developed porosity structure, and higher reaction activity than D001-CC and D72. The effects of reaction temperature, DMM/CH2O molar ratio, reaction time, and catalyst loading were studied with NKC-9. A possible mechanism was explored to describe the bond reorganizations during the reactions.