The invention relates to the field of medicines, and provides an injection fluorouracil lyophilized agent and a preparation method thereof. The method comprises the steps that according to a formula,fluorouracil, edetate disodium, sodium hydroxide, mannitol, water for injection and activated carbon are weighed for preparing ingredient liquid; filtering is conducted to remove the activated carbonin the ingredient liquid, and filter liquid is subjected to filling and semi-plugging according to a preset specification to obtain a filled semi-finished product; the semi-finished product is subjected to lyophilization treatment, lyophilization treatment comprises the steps that the semi-finished product is placed in a lyophilization device, pre-freezing is conducted at -45 DEG C to -40 DEG C for 1.5-2 hours, within 0.5-1 hour, temperature is elevated to -15 DEG C to -18 DEG C, and is maintained for 1-2 hours, within 0.5-1 hour, the temperature is reduced to -45 DEG C to -40 DEG C, and is maintained for 2.5-3 hours, after vacuumizing is conducted, within 1-1.5 hours, the temperature is elevated to 0-1 DEG C, and is maintained for 35-40 hours, the temperature is elevated continuously to 33-37 DEG C, and is maintained for 8-10 hours for desorption drying, and a whole plug is pressed to obtain the lyophilized agent. The lyophilized agent has good solubility, clarity and stability, and is beneficial for safe clinical administration.