Under the appeal of carbon peaking and carbon neutrality goals, it is highly advisable to develop green chemical technologies. Based on this, it is even more attractive to synthesize methanol with the H-2 generated from water electrolysis by offshore wind power and the CO2 separated from offshore CO2-rich natural gas. Therefore, the separation and adsorption of CO2-rich natural gas in this context is of great socioeconomic significance. However, the conventional high-throughput screening methods for metal-organic frameworks (MOFs) in separating natural gas components and CO2 suffer from great challenges such as high model complexity and long computation time. To address the aforementioned problems, a machine learning-assisted modeling and screening strategy is proposed herein for the rapid and efficient separation of CO2 from the actual natural gas of six components (N-2, CO2, CH4, C2H6, C3H8, and H2S). First, structural analysis is used to eliminate the MOFs that cannot adsorb CO2 from the Computation-Ready Experimental Metal-Organic Frameworks (CoRE-MOFs) database. Six structural and 17 chemical descriptors of the remaining MOFs were calculated. Grand Canonical Monte Carlo (GCMC) simulations were applied to evaluate the separation performance metrics of the randomly selected training and testing MOF samples. By combining 23 descriptors and separation performance metrics, a Random Forest (RF) regression model was obtained with R-2 exceeding 0.92 on the test samples, which was employed to predict the separation performance of the remaining MOFs. As a result, 10 MOF candidates with the best CO2 separation performance were obtained. Furthermore, a structure-property relationship of MOFs with satisfactory regenerability was conducted. Three design strategies were proposed to guide the development of high-performance novel MOFs for CO2 separation. This study offers a high-throughput screening framework for MOFs to facilitate the separation of CO2 from a CO2-rich natural gas.