To achieve unique molecular‐recognition patterns, a rational control of the flexibility of porous coordination polymers (PCPs) is highly sought, but it remains elusive. From a thermodynamic perspective, the competitive relationship between the structural deformation energy (Edef) of soft PCPs and the guest interaction is key for selective a guest‐triggered structural‐transformation behavior. Therefore, it is vital to investigate and control Edef to regulate this competition for flexibility control. Driven by these theoretical insights, we demonstrate an Edef‐modulation strategy via encoding inter‐framework hydrogen bonds into a soft PCP with an interpenetrated structure. As a proof of this concept, the enhanced Edef of PCP enables a selective gate‐opening behavior toward CHCl3 over CH2Cl2 by changing the adsorption‐energy landscape of the compounds. This study provides a new direction for the design of functional soft porous materials.