In order to balance the contradiction between mesopore introduction and loss of microporosity, a surface modification strategy is proposed by selectively adsorbing organic alkaline molecules on Beta molecular sieves before NaOH etching. Organic alkaline molecules adsorb on framework aluminum sites and the protective function of organic bases is affected by the adsorption configuration and physical barrier effect of organic bases. Organic alkaline molecules serve as a protective agent to increase the bond length of Al-O bonds. Therefore, the as-synthesized hierarchical Beta molecular sieves have more acid sites due to the preservation of aluminum atoms. When employed as catalysts in the dehydration reaction of glucose, 5-hydroxymethylfurfural (5-HMF) is obtained under the synergistic effect of Brønsted and Lewis acid sites. The unique contribution is to realize the porosity regulation and alleviate the acidity loss of Beta molecular sieves. These results are important to broaden the application fields of aluminum-silicon molecular sieves especially for large molecule-engaged acid catalyzed reactions.