Using two typical experimental methods, differential scanning calorimetric (DSC) analysis and Fourier Transform Infrared (FTIR) spectroscopy, we have studied the effect of single wall carbon nanotubes (SWCNTs), both amide functionalized (f–SWCNTs) and non-functionalized pristine (p-SWCNTs), on the thermal and structural properties of the SOPC phospholipid. We proposed and discussed possible physical mechanisms driving the thermodynamic and structural states of the bionanocomposites – SOPC/pSWCNTs and SOPC/f-SWCNTs. By FTIR spectroscopy, we demonstrated that p-SWCNTs have less affinity to create and sustain hydrogen bonds polpulaion with the phospholipids carbonyl groups than of the f-SWCNTs. The asymmetric shape of the thermal peaks in the DSC curves suggests the presence of an intermediate state, between gel and liquid crystal, revealing the non-completeness of the transition characterized by the competition of van’t Hoff enthalpy and the calorimetric one. To gain insights into the SOPC molecule’s structure fluctuations with time, in the presence of functionalized and non-functionalized carbon nanotubes, we consider conformational fluctuations able to alter the thermal and spectral characteristics of the single molecule. The time between two non-correlated fluctuating conformational structures was used to assess the dynamic conformational evolution. We found that SOPC/f-SWCNTs is more stable than that of SOPC/p-SWCNTs due to the effective hydrogen-bonding role of the amide radical. Considering, the level of interdigitation of the hydrocarbon chains, we found that the liquid crystal-gel phase transition is more likely a transition between the non-interdigitated liquid crystals and an interdigitated gel phases.