The invention relates to the field of medical checkup quality control, and concretely relates to a liquid composite protective agent for long-term culture preservation, and a preparation method and an application method thereof. The liquid composite protective agent for long-term culture preservation is prepared from the following components according to 100mL of solution agent: 15 to 20mL of ethylene glycol, 10 to 15mL of glycerinum, 0.5 to 1g of nutrient bouillon, 0.3 to 0.8g of trehalose, 0.1 to 0.5g of brain infusion powder, and the balance distilled water. The liquid composite protective agent for long-term culture preservation provided by the invention has good protection on various bacteria cultures, can ensure the activity of the cultures at the temperature being minus 20 DEG C and below after being mixed with the cultures, cannot affect the biochemical characters of microorganisms, has no need to be freeze-dried, redissolved and preserved in dark, and is convenient to use and operate in clinic bacterial detection. The cultures protected by the liquid composite protective agent provided by the invention can stably survive for more than 1 year at the temperature being minus 20 DEG C, and stably survive for more than 10 years at the temperature being minus 70 DEG C, so that great convenience is provided for the long-term preservation of special cultures.