The invention discloses a cleaning solution for removing calcium carbonate scale and a preparation method and application of the cleaning solution, and belongs to the field of chemical descaling. Thecleaning solution comprises, by mass, 3%-8% of phosphorus-free organic acid complexing agent, 10%-25% of phosphorus-free chelating agent, 2%-6% of penetration cosolvent, 0.05%-0.15% of corrosion inhibitor, and the balance water. The corrosion inhibitor is oleic acid imidazoline corrosion inhibitor and / or thiazole corrosion inhibitor. The penetration cosolvent is prepared by the following steps that anionic surfactant, polyols and clean water are added into a reaction still and heated to 30-50 DEG C, stirring is conducted for 20-40 minutes, sodium hexametaphosphate, sodium but and the clean water are added, the temperature is reduced to 15-25 DEG C, stirring is conducted for 30-50 minutes under the constant temperature conditions, and the penetration cosolvent is obtained; and the mass ratio of the anionic surfactant, the polyols to the clean water added for the first time is 1:10-20:20-30, the mass ratio of the sodium but, the sodium hexametaphosphate to the clean water added for the second time is 1:40-50:80-200, and the mass percent of the sodium but accounted for the penetration cosolvent is 0.16-0.3%. The cleaning solution is high in scale dissolving rate, good in scale inhibition effect, safe and environmentally friendly, and good in biodegradability.