The invention provides core-shell lightweight aggregate and a preparation method thereof. The core-shell lightweight aggregate comprises a core and a shell according to a mass ratio of 1:1-2:1, the core comprises, by weight, 65-85% of sludge, 6-12% of calcium superphosphate, 5-10% of potassium sulfate, 3-8% of manganese nitrate, 5-11% of ammonium phosphate and 4-10% of sodium chloride, and the shell comprises, by mass, 75-85% of polluted soil, 10-15% of sludge and 5-10% of glass powder. The preparation method includes: adopting the sludge as a main raw material, and adding inorganic salt and phytonutrient containing nitrogen and phosphorus to prepare the core; adopting the polluted soil as a main raw material, and adding the glass powder which is a sintering aid to prepare the shell; coating the shell onto the core by means of high-temperature sintering. Recycling rate of solid waste like the sludge and the polluted soil is increased, the lightweight aggregate suitable for plant hydroponics is developed, and the lightweight aggregate is of quite important economic, environment-protection and scientific-research significance.