The invention relates to a novel magnetic molecular targeted ultrasound contrast agent, in particular to a gas-wrapped magnetic liposome microsphere suspension with the mean diameter of 1-4 micrometers and a preparation method thereof. The preparation method of the magnetic molecular targeted ultrasound contrast agent microsphere comprises a condition that a lipid layer of the microsphere and/or the surface of the lipid layer contains (or connects) magnetic response materials. A contrast agent microsphere wall material contains phospholipids, polyethylene glycol (PEG), PEG phospholipid polymers, biotinylated and/or polypeptide modificatory PEG phospholipid polymer, poloxamer, ligands (monoclonal antibodies or polypeptide, and the like) and the magnetic response materials and/or avidin bridging materials, wherein the ligand (monoclonal antibodies or polypeptide, and the like) has specific affinity to target molecules, the wrapped gas is a fluorine carbon gas, and a solvent is an aqueous medium (distilled water). The invention also provides the preparation method of the magnetic molecular targeted ultrasound contrast agent microsphere, which comprises a condition that the specific ligand is connected with the microsphere in a covalence and avidin bridging way. The novel magnetic molecular targeted ultrasound contrast agent has good targeted developing effect, can be used for evaluating the change of vessel endothelial molecules of an arterious and venous system of an organic tissue and has good application prospect in treatment.