The organization of microporous space in zeolites is discussed. A new step-by-step model is proposed that explains the principles of organizing the hierarchy of microporous space at the stage of assembling zeolites from elements of minimal size: a primary building unit, secondary building units, tertiary building units or building polyhedra, a sodalite cage, and a supercage. To illustrate the stepwise hierarchical porous structure of nanomaterials, the following zeolites with small and large micropores have been selected as the model objects: sodalite (SOD, the maximum diameter of a sphere that can enter the pores is 0.3 nm) and zeolites of type A (LTA, the maximum diameter of a sphere that can enter the pores is 0.41 nm), type X, Y (FAU, the maximum diameter of a sphere that can enter the pores is 0.75 nm), and type BETA (the maximum diameter of a sphere that can enter the pores is 0.67 nm). Two-dimensional and three-dimensional modeling in 3Ds Max software was used. We believe that such an approach will be useful for developing ways to create complex zeolite compositions for specific applications, such as catalysis, where the geometry of the pores determines the size of the molecules entering the voids and computer modeling can play an important predictive role. This work takes a look at specific aspects of using the heat desorption method to study mesoporous materials with a BETA zeolite as an example and presents the results of experimental research into the characteristics of the porous structure of hierarchically structured zeolite materials (specific surface area 180–380 m2/g, external surface area 120–200 m2/g, micropore volume 0.001–0.1 mL/g).