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Coenzyme Q10 (CoQ10) is an endogenous, lipophilic quinone compound that functions as an electron carrier in the mitochondrial respiratory chain and plays a pivotal role in cell metabolism. Despite its numerous important physiological functions, the practical application of CoQ10 is limited due to its high molecular weight, poor water solubility, photolability, chemical instability, and low bioavailability. To overcome these challenges, we developed a solid dispersion formulation of protamine loaded CoQ10 (CoQ10/Pr) using an efficient mechanochemical technology without solvents. Protamine was used as carrier and poloxamer 188 as solubilizer, while butylated hydroxytoluene (BHT) and micro powder silica gel were utilized as stabilizers and lubricants. The optimal ball milling condition to prepare CoQ10/Pr was at 100 r/min for 4 hours. The treated CoQ10/Pr has exhibited rapid-release properties, with significantly enhanced water solubility by 392,000 times, and bioavailability by 0.68 times. Furthermore, the treated CoQ10/Pr became resistant to moisture, high temperature and strong light, which makes it suitable for long-term storage. The molecular docking suggested that the solubilization mechanism of CoQ10 was closely associated with the encapsulation and complexation of protamine, as well as the formation of an intermolecular complex through hydrogen bond between CoQ10 and arginine residues on protamine. In summary, the CoQ10 solid dispersion formulation enjoys advantages such as excellent water solubility, stability, bioavailability, and low cost. This formulation also meets the stringent quality requirements of products in the food, cosmetic, and health industries. It offers dual benefits in both theoretical research and industrial development.