The possibility of coexistence of multiple isomers for zirconium bis(phenoxy-imine) catalyst has been systematically studied by computational approaches. The energetics among the five different isomers of neutral Zr-catalyst have been assessed quantum mechanically. The results suggest that isomer cis-N/trans-O/cis-Me is the most stable among the five isomers in accordance with the general observations of these kinds of phenoxy-imine catalyst. However, for the polymerization reaction, the active species is known to be the cationic form of the Zr-catalyst. The Zr-cation can exist in three different isomers, viz., cis-N/trans-O (A), cis-N/cis-O (B), and trans-N/cis-O (C), and the presence of flexible ligands makes the modeling considerably challenging to determine the most preferable isomers. For the efficient modeling, altogether 80 different structures for each of the three cationic isomers have been generated by using molecular dynamics simulations, and subsequently, the quantum mechanical optimization of these structures has been performed to obtain the most preferable conformation for each isomer. The existing probability derived from the obtained free energy values suggests that isomer C is comparable with isomer A. Even more, isomer A of the cation can be present in two different conformations, where the orientation of side groups is altered at the imine nitrogen atoms. The transition state calculations also confirm that the Zr-cation can exist as a mixture of three structures, "up-down" and "down-down" orientations of the isomers A along with isomer C's "up-up" orientation. However, by varying the substituents at imine nitrogen atoms, one could modulate multimodal to unimodal polymerization behavior of the Zr-catalysts. We believe that this study should provide a starting point for theoretically exploring the mechanistic pathway of the complicated polymerization reactions.