The invention discloses a compound water soluble fertilizer used for citrus crops, a preparation method and an application method. The compound water soluble fertilizer used for citrus crops is mainly used in plant nutrition field, and comprises the following components: an amino acid raw material, macroelements P and K, secondary elements Mg and Ca, trace elements Fe, Mn, Zn, B, Mo and Cu, a beneficial element Si, an auxiliary agent, a PH conditioning agent and an aqueous solution. The preparation method is characterized in that composite amino acid chelates Mn, Fe, Cu, Mg, Ca and Zn at normal temperature of 15-35 DEG C and prepares the water soluble fertilizer with six metallic elements, the reasonable fertilizing can be carried out at different growth period of the crops, the balance supplement of a plurality of nutrient elements required by citrus crops can be realized, and the output and quality of the citrus crops can be increased.