The analysis of the fluid cross-flow characteristics in partially filled cavities is essential for characterizing the fluid flow behaviors in deep marine carbonate reservoirs. Thus, it is vital for the effective development of crude oil in deep marine carbonate reservoirs. This study presents mathematical models for portraying the fluid cross-flow characteristics in partially filled cavities, considering the effects of gravity, cavity filling degree, and storability ratio. By solving the models using the Laplace transformation and Stehfest numerical inversion methods, pressure transient analysis, and rate transient analysis can be performed on the reservoir, resulting in the evaluation of the dimensionless pressure, dimensionless cross-flow rate, and dimensionless cumulative cross-flow rate in a cavity. The available experimental data adequately validate the proposed models. Moreover, based on the derived model, parameter sensitivity analysis is conducted. Based on the results, the cross-flow characteristics are significantly affected by fluid and cavity parameters. Additionally, as the thickness-to-radius ratio of the cavity decreases, the radial flow becomes pronounced, leading to a more complicated cross-flow process. The derived model not only assists in understanding and predicting the cross-flow characteristics in partially filled cavities in deep marine carbonate reservoirs but also provides guidance for crude oil exploitation.