Chemical agglomeration is presented as a promising process to reduce the submicron particles and SO3 in a coal-fired power plant, which uses a chemical agent to induce particles and SO3 agglomerate and improves the removal efficiency of electrostatic precipitation (ESP). In this study, an experimental plant containing a chemical agglomeration chamber connected to an ESP unit has been built to investigate the particles and SO3 removal effect. The results showed that chemical agglomeration technology increased the average size of particles and the fine particle and SO3 concentration reduced at the ESP outlet; the improvement of collection efficiency was over 5%-20%. The removal mechanism was investigated by Density Functional Theory (DFT) calculations at the molecular level, the reasonable calculation model with pectin as agglomeration agent was established, and the interactions between SO3, H2SO4, SiO2, and pectin were, explored. In the results, adsorption ability of pectin for H2SO4 is better than SiO2, and relative energy of complex between H2SO4 and TOS is lower than H2O. Meanwhile, we also studied chemical structures, atomic charges, and molecular orbitals to explore their basic properties. Combining computational and experimental results together, the fine particle and SO3 mechanism with pectin adsorption can be determined.