Magnolol is a natural compound extracted from the traditional Chinese medicine Magnolia officinalis, which exhibits antimicrobial properties. However, magnolol is insoluble in water and consists of a phenolic hydroxyl group, which is volatile; these factors hinder its application. In this study, a safe and environmentally friendly method to improve the microbial resistance and storability of harvested fruits is developed using the water-soluble carrier carboxymethyl chitosan (CMCS) and magnolol. Magnolol was loaded on CMCS particles to form Magnolol@CMCS antimicrobial particles, a preservation coating agent. Magnolol@CMCS particles effectively solved the problems of water insolubility and agglomeration of magnolol and reduced the size distribution D50 value of magnolol from 0.749 to 0.213 μm. Magnolol@CMCS particles showed greater toxicity against Staphylococcus aureus, Escherichia coli, and Botryosphaeria dothidea than that of magnolol alone, with effective medium concentration (EC50) values of 0.9408, 142.4144, and 8.8028 μg/mL, respectively. Kiwifruit treated with the Magnolol@CMCS solution showed delayed changes in fruit hardness and soluble solid and dry matter contents and significantly higher ascorbic acid (vitamin C) and soluble total sugar contents and sugar:acid ratios compared with that of the control fruit. In addition, no disease spots were observed on fruit treated with the Magnolol@CMCS solution within 7 days after inoculation with B. dothidea. In conclusion, Magnolol@CMCS particles showed antimicrobial activity on harvested fruits, effectively delayed the hardness and nutritional changes of fruits during storage, and improved the storability of kiwifruit.