In this article, we designed and synthesized an amino-functionalized hybrid hydrocarbon/fluorocarbon double-chain phospholipid (ACFPC) containing one chain with the hydrophobic fluorocarbon chain and terminal amino, amide, and ether linkages and one chain with the hydrocarbon chain. The novel reactive phospholipid was fully characterized with Fourier transform infrared spectroscopy (FTIR), nuclear magnetic resonance spectroscopy (NMR), and mass spectrometry (MS). Then the self-assembly behaviors of the hybrid double-chain phospholipid in aqueous and acidic media were investigated with transmission electron microscopy (TEM), the critical micelle concentration (cmc), dynamic light scattering (DLS), and the hydrocarbon double-chain phospholipid (ACCPC) for comparison. Moreover, their self-assembled structures in aqueous and acidic media were simulated using the dissipative particle dynamics (DPD) method. These results suggest that the fluorocarbon/hydrocarbon hybrid-chain phospholipid can self-assemble into a more stable microstructure compared to the double hydrocarbon chain phospholipid, which will have the potential ability to self-assemble into a more stable minicking biomembrane structure onto material surfaces to inhibit protein adsorption under complicated physiological conditions.