Investigations on the structural transition and property of the intermediate structures are significant to understand the gas adsorption and separation performance in flexible metal-organic frameworks (MOFs). Herein, theoretical investigations were conducted to track CO2/N-2 adsorption and separation in the flexible bridged phenyl MOF 1. Results showed the closed pore form 1B expanded and exhibited the intermediate states of 1B_x (x = 9.8, 10.34, 11.3, 12.5, and 14.1) with the adsorption of CO2. The adsorption performance-structure-pressure relationship was built based on the adsorption isotherms, and 1B_9.8, 1B_10.34, 1B_11.3, 1B_12.5, and 1B_14.1 were the structures of 1B with adsorbed CO2 at 26.3, 29.2, 29.5, 33.7, and 37.1 bar at 298 K, respectively. The CO2/N-2 selectivity was plotted based on the structure-pressure relationship. The interaction and gas distribution analyses demonstrated that the adsorption site changed during the structural transition in the adsorption process, which played a significant role in CO2 adsorption and separation. This work provided significant guidelines for elucidating the gas adsorption and separation in flexible adsorbent materials.