A fundamental understanding of the versatile and tunable nanostructuration effect of two phosphonium ionic liquids (ILs), denoted octadecyltriphenylphosphonium iodide (IL-C18) and tributyl(methyl)phosphonium methylsulfate (IL-108), on a semicrystalline fluorinated copolymer poly(vinylidene fluoride-co-chlorotrifluoroethylene) (P(VDF-CTFE)) was elaborated. This research suggests that the nanostructuration mechanism is very dependent on the diffusion and interacting abilities of ILs in matrix, which are determined by the chemical structures of ILs. Both LLs appear to diffuse and regularly assemble in the rigid amorphous fraction (RAF) of P(VDF-CTFE) between crystalline lamellae thanks to the "template" confinement effect of 2D structure. The assembled structure shows a gradually regular ID to 2D geometric evolution with increasing the ILs amount revealed by Porod exponents in SANS analyses. Simultaneously, these regularly assembled ILs in the RAF also act as "template" to efficiently induce a complete transition of nonpolar alpha-phase to polar gamma- and/or beta-phase with only a tiny amount of ILs (from 2 wt %) (by XRD and FTIR). Moreover, the crystallization displays a depression behavior with reduced T-c, T-m, crystallinity (by DSC), and crystallite size (by SANS) due to the existence of ILs in the RAF seen as obstacle for the regular chain-folding and the dipolar interaction with P(VDF-CTFE). We propose that the synergistic influence of mutual "templates" endues phosphonium ILs a versatile nanostructuration on the fluorinated matrix. Moreover, this versatile nanostructuration effect can be easily tuned by tailoring the chemical structures of ILs. The difference in the chemical structures of ILs endows them different diffusion rates upon crystallization from solution for preparing resulting blend films and strengths of dipolar interaction with P(VDF-CTFE), consequently affecting their dispersion state in the matrix to reside in the RAF with different extents and interacting abilities (confirmed by IDEA and DMA). Thus, IL-108 with faster migration rate and stronger dipolar interaction than IL-C18 (due to the smaller steric hindrance and extra polar groups in the cation/anion combination of the IL structure) locates in the RAF much more to induce more trans-configuration (beta-phase), more homogeneous dispersion morphology, and higher depression of crystallization.