To replace traditional phthalate plasticizers, our previous research revealed that trioctyl citrate (CA) with an alkyl chain containing 8 carbon atoms (C8) exhibited excellent plasticizing properties. In order to delve deeper into the plasticization effects of CA isomers, CA with different side‐chain structures (C8‐Line, C8‐Branch, and C8‐Star) were synthesized by esterification reactions, and various CA/polyvinyl chloride (PVC) composite films with different CA contents were prepared using a solution casting method. The plasticization mechanisms of these isomers were systematically explored through experimental and molecular dynamics simulations. The results indicate that C8‐Branch demonstrates the optimal plasticizing effect, followed by C8‐Line, while C8‐Star exhibits poorer performance. The C8‐Branch/PVC composite system displays the best plasticizing effect, attributed to the strong interaction forces between the Cl atoms of PVC and the COO groups of CA. On the contrary, the formation of stable dipole pairs between C8‐Star and PVC is impeded by steric hindrance effects. The interaction between the two is predominantly dependent on the intertwining of the alkyl chains in C8‐Star with the PVC chains, also elucidating the observed higher migration rate in the C8‐Star/PVC system. This study provides technical guidance and theoretical basis for the optimized design of high‐performance CA/PVC composites.