When CO2 saline aquifer storage is carried out, the heterogeneity of reservoir rock is an important factor affecting CO2 transport, and the reservoir heterogeneity in numerical simulations is mainly manifested as the heterogeneity of the parameter field. Since the parameter distributions across the reservoir are not available with the existing probes, the stochastic finite element method is combined with a two‐phase flow model to establish an unconditional random field of permeability, and computations are performed using the Monte Carlo method. The permeability, CO2 maximum migration distance (Md) and CO2 sweep area (Sa) were analyzed for mutual correlation. The permeability correlation area affecting Md and Sa was obtained, and the changes in the correlation area under the coefficient of variation (Cv) and correlation length (λx) of the permeability field in the different reservoirs were analyzed. The kriging superposition approach (KSA) was subsequently used to estimate both the Md and Sa of the target reservoir by establishing conditional random fields based on the sampling parameters in regions with different correlations, resulting in errors of 0.66% for Md and 0.96% for Sa in the high correlation region and 4.86% and 3.12% for Md and Sa in the low correlation region, which suggested that the sampling results from the high correlation region were less biased in the estimation. Under limited sampling conditions, it is recommended that samples be collected in regions with high correlations to reduce the uncertainty of CO2 transport analysis due to unknown heterogeneity. © 2024 Society of Chemical Industry and John Wiley & Sons, Ltd.