The invention discloses a preparation method of a soil conditioner being rich in citric acid soluble silicon. The preparation method includes the steps of: 1) synthesizing sodium calcium silicate from a substance being rich in silicon dioxide and a substance with calcium oxide being a main component as raw materials in a hydrothermal manner; 2) decomposing the sodium calcium silicate in a dilute alkaline solution to obtain calcium silicate; 3) washing and drying the calcium silicate to prepare the soil conditioner being rich in citric acid soluble silicon. The soil conditioner is not less than 30.0% in content of citric acid soluble silicon and is more than 90% in silicon effective rate. Water storage capability of the calcium silicate is more than 17 times as that of soil in the same mass. In addition, the raw material of the soil conditioner can be obtained from large-quantity industrial solid waste, such as fly ash, and also can be obtained from primary resources with the main component being silicon dioxide. The raw material is very wide in sources.