Pore structure is a crucial factor affecting the physical properties of porous materials, and understanding the mechanisms and laws of these effects is of great significance in the fields of geosciences and petroleum engineering. However, it remains a challenge to accurately understand and quantify the relationship between pore structures and effective properties. This paper improves a workflow to focus on investigating the effect of pore structure on physical properties. First, a hybrid modeling approach combining process-based and morphology-based methods is proposed to reconstruct 3D models with diverse pore structure types. Then, the characteristics and differences in pore structure in these models are compared. Finally, the variation laws and pore-scale mechanisms of the influence of pore structure on physical properties (permeability and elasticity) are discussed based on the reconstructed models. The relationship models between pore structure parameters and permeability/elastic parameters in the grain packing model are established. The effect of pore structure evolution on permeability/elasticity and the microscopic mechanism in three types of morphology-based reconstruction models are explored. The influence degree of pore structure on elastic parameters (bulk modulus, shear modulus, P-wave velocity, and S-wave velocity) is quantified, reaching 29.54%, 51.40%, 18.94%, and 23.18%, respectively. This work forms a workflow for exploring the relationship between pore structures and petrophysical properties at the microscopic scale, providing more ideas and references for understanding the complex physical properties in porous media.