We introduced a small molecular "inducing ligand" strategy to crystallize proteins via dual noncovalent interactions. Here we demonstrate that the variant protein-packing frameworks of concanavalin A (ConA) binding with ligands are controlled by different crystallization methods. Besides, the protein crystalline frameworks are also controlled by small-molecule inducing ligands RnM (n = 1-5), which varies in the number of ethylene oxide repeating units. To better understand the mechanism of different packing frameworks controlled by different inducing ligands, all-atom molecular dynamic (MD) simulations were performed. The MD simulation focused on the dynamic dimerization behavior of ConA-RnM system, which revealed clear relationships between the length of inducing ligands and ConA crystalline. In short, besides protein-packing framework control via different crystallization methods, inducing ligands RnM with suitable spacer lengths (n = 3, 4) also play an important role in desired and stable crystalline frameworks.