The invention discloses N3-ortho toluene formoxyl uracil nanosuspension and lyophilized preparation thereof, which belong to the technical field of medical drugs. The preparation method of the lyophilized preparation of the N3-ortho toluene formoxyl uracil nanosuspension comprises the steps of (1) dispersing surface active agents into water solution to obtain solution A; (2) dispersing N3-ortho toluene formoxyl uracil into the solution A to obtain injectable suspension B; (3) shearing the injectable suspension B at high speed to obtain foremilk C; (4) enabling the quality of the foremilk C tobe even through a milk evening machine to obtain the N3-ortho toluene formoxyl uracil nanosuspension; and (5) adding lyophilized protective agents into the nanosuspension, filtering and degerming, lyophilizing and drying to remove water, and obtaining the lyophilized preparation of the N3-ortho toluene formoxyl uracil nanosuspension. The nanosuspension prepared by the preparation method is uniform in appearance quality with average grain diameter of 50-200nm, high in dissolution rate and capable of being prepared into injection or oral preparation of tablets, capsules and the like in special application.