In this study, the effect of α-tocopheryl malonate (TM) on physical and structural properties of DPPC liposomes was investigated using ANS fluorescence, DPH, and TMA–DPH anisotropy fluorescence and differential scanning calorimetry (DSC) methods. The presence of embedded TM in DPPC liposomes caused alteration in its phase transition temperatures, structural order, dynamics, and hydration of head groups increasingly with growing TM concentration. The ANS fluorescence results demonstrated that increasing TM presence in the DPPC gel phase due to interrupted membrane structure caused the formation of new binding sites. Temperature investigations in the range of 20 °C to 60 °C showed that increasing temperature rises ANS fluorescence which reaches local and global maxima at 36 °C and 42 °C, respectively. The rising TM concentration at the phase transition temperature of DPPC led to the lowering of ANS fluorescence, indicating a decreased binding of ANS. Simultaneously, during heating, a roughly 10-nm shift of ANS emission maximum was observed. The results indicated that in the fluid phase, the observed quenching appears as a result of increasing accessibility of water molecules into ANS in this region. The DPH results indicated that in the gel phase presence of TM introduced disorder in the hydrophobic acyl chain region led to its fluidization. The TMA–DPH results indicated an increasing disorder in the interface region and an increasing hydration of head group atoms at the surface of the membrane. The increasing concentration of TM results in the formation of multicomponent DSC traces, suggesting the formation of another structural phase. The applied methods proved that the incorporation of TM into DPPC membrane results in the interaction of malonate moiety with DPPC head group atoms in the interphase layer and induces the interruption in the membrane packing order, leading to its structural changes. The presented results show that TM presence could regulate the membrane properties, thus it may indicate one of the possible mechanisms responsible for the effective disruption of cell membranes by TM. The knowledge of molecular mechanism how TM interacts with the membrane will help to elucidate its possible pharmacological activity.