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The development of shale gas necessitates accurate modeling and characterization of these complicated formations, at both small and large scales. At the small scale, the studies based on experimental techniques have uncovered that the components and pore types in shales vary dramatically. Several pore types are identified and varied when the thermal maturation of shales changes. Therefore, accurate modeling and characterization of shale samples require taking such dynamic variations into consideration. This study presents a novel, dynamic, and three-dimensional (3D) modeling technique considering pore-system variation when the thermal maturation changes. The technique can construct dynamic shale models based on quartet structure generation set algorithm and morphological operation. This method can include various elements available in the shale samples in a very accurate way when the dynamic processes are reproduced. To evaluate the performance of the presented technique, 12 dynamic 3D shale models of three cases are constructed. These models are then characterized by analyzing the fractions of components and pores, pore and throat size distributions, coordination number distribution, fractal dimension, and tortuosity. Besides, gas transport in these dynamic 3D shale models is also simulated using pore network modeling to demonstrate the permeability variation of these models. Moreover, the fractions of interparticle and intraparticle pores and cementation degree are changed to further illustrate the capability of the developed algorithm. This study reveals such a dynamic modeling technique is a robust tool to construct various porous media with complicated elements and pores, which is not limited to shale samples. Key Points:• A novel, dynamic, and three-dimensional modeling technique considering pore-system evolution was presented • Generated shale models were characterized by analyzing the geometric, topological, and transport properties of pore systems • The simulation of the gas flow in shale models considers the viscous flow, Knudsen diffusion, and surface diffusion Correspondence to: