Defect passivation using two-dimensional (2D)-layered perovskites with organic spacers on 3D bulk perovskites has been proposed as an effective strategy to improve perovskite solar cell stability and efficiency. Specifically, fluorination of the organic spacers has been employed due to the resulting hydrophobic nature and the defect passivation characteristics. In addition to the type of functional groups attached to the spacer molecules, conformational changes of fluorine isomers on layered perovskites can provide an extended strategy to control a variety of opto-electrical properties related to the interlayer spacing. As a model system for the structural isomer of fluorinated spacers, meta-CF3 and para-CF3 groups anchored to phenethylammonium iodide (PEAI) spacer molecules are employed to synthesize 2D perovskites and to investigate their full potential as an interfacial modifier for perovskite solar cells. The fluorination position change leads to altered opto-electrical characteristics in layered perovskites. Although they possess identical functional groups, the different orientations of the functional groups used in the perovskite layer deposited on the 3D perovskite absorber result in distinct electrical properties of 2D/3D heterostructures due to dissimilar intermolecular interactions. The 2D perovskite with meta-CF3-PEAI spacers exhibits an enhancement of the charge transport in the out-of-plane orientation and an improved suppression of the trap states of 3D perovskites while also providing a more favorable energy alignment for efficient charge transfers. Theoretical simulations are consistent with the experimental results. The structural isomers of fluorination anchoring to spacer cations alter the structural configuration of the spacer as well as the interlayer spacing that can improve the performance and the stability of 2D/3D perovskite solar cells.