Underground CO₂ storage is a promising technology for mitigating climate change. In this vein, the subsurface condition was inherited a lot of uncertainties that prevent the success of the CO₂ storage project. Therefore, this study aims to build the 3D model under geological uncertainties for enhancing CO₂ storage capacity in the Shahejie Formation (Es1), Nv32 block, China. The well logs, seismic data, and geological data were used for the construction of 3-D petrophysical models. The target study area model focused on four units (Es1 × 1, Es1 × 2, Es1 × 3, and Es1 × 4) in the Shahejie Formation. Well logs were utilized to predict petrophysical properties; the lithofacies indicated that the Shahejie Formation units are sandstone, shale, and limestone. Also, the petrophysical interpretation demonstrated that the \(Es1\) reservoir exhibited high percentage porosity, permeability, and medium to high net-to-gross ratios. The static model showed that there are lateral heterogeneities in the reservoir properties and lithofacies; optimal reservoir rocks exist in Es1 × 4, Es1 × 3, and Es1 × 2 units. Moreover, the pore volume of the Es1 unit was estimated from petrophysical property models, ranging between 0.554369 and 10.03771 × 10⁶ sm³, with a total volumetric value of 20.0819 × 10⁶ sm³ for the four reservoir units. Then, the 100–400 realizations were generated for the pore volume uncertainties assessment. In consequence, 200 realizations were determined as an optimal solution for capturing geological uncertainties. The estimation of CO₂ storage capacity in the Es1 formation ranged from 15.6 to 207.9 × 10⁹ t. This result suggests the potential of CO₂ geological storage in the Shahejie Formation, China.