Hydrogen doping using existing natural gas pipelines is a promising solution for hydrogen transportation. A large number of non-metallic seals are currently used in long-distance natural gas pipelines. Compared with metallic seals, non-metallic seals have the advantages of corrosion resistance, light weight, and easy processing, which can improve the safety and economy of pipelines. In order to ensure the long-term safe use of seals in hydrogen-doped natural gas pipelines, this paper selects the non-metallic seals commonly used in long-distance natural gas pipelines and carries out the hydrogen-doped sealing test, hydrogen-doped aging test, and hydrogen-doped anti-explosion test on the non-metallic seals under the conditions of different hydrogen-doped ratios. At the same time, combined with the actual working conditions of a hydrogen-doped natural gas pipeline, the external environment, and other factors, the applicability evaluation index system was established, and the applicability evaluation model based on hydrogen-doped physical and chemical properties, fuzzy comprehensive evaluation, and the structural entropy weight method was developed and applied in the field. The results show that the evaluation result of nitrile rubber in soft seals is 1.7845, and the evaluation result of graphite-polytetrafluoroethylene material in hard seals is 1.5988, and both of them are at a good level. This paper provides technical support and judging strategies for the selection of non-metallic sealing materials for hydrogen-doped natural gas pipelines.