The present study reports a design of a unique holder for modifying the structure of ZSM-5 zeolite using electron beam generated from an industrial UERL-10-15S2 linear accelerator with a fixed energy of 10 MeV. The design was made based on a unique holder, named EDSCholder, which can be simultaneously used as the beam energy degrader and the sample container. Metal materials with different thicknesses and geometries were utilized for simulating and designing (using the Monte-Carlo N particle code) such a EDSCholder. In particular, a mathematical formula was proposed for correcting the energy distribution of the electron beam generated from the accelerator, which is not precisely mono-energetic. By comparing the simulated results with the experimental data, we found that the 1050 aluminum alloys with thicknesses of 2.5, 4.7, and 6.8 mm and having a cylindrical geometry are optimal for generating the electron energies of 9.00, 8.04, and 7.12 MeV, respectively. It was also found that, by using a rotated-cylinder EDSCholder in combination with the scanning process of the linear accelerator, one can produce a homogeneous dose rate distribution in the samples, which is similar to that obtained by using a parallel electron beam. For the structural modification of ZSM-5 zeolite using the above rotated-cylinder EDSCholder, the simulated results indicated that the sample thickness in the range of 2.5−3 cm can ensure the uniformity of absorbed dose in the irradiated samples. In addition, the influence of sample density (in a range of 0.65−0.85 g/cm3) and contribution of the X-ray scatterings to the absorbed dose was found to be insignificant and negligible. Moreover, our present design is able to significantly shorten the irradiation time as compared to the conventional design for irradiation using a traditional conveyor system. Hence, this paper proposes an effective solution to reduce the operation cost and enhance the applicability of industrial electron beam accelerators to the structural modification of materials.