The invention relates to a synergistic composition for water soluble fertilizer and its preparation method and an application and belongs to that technical field of water soluble fertilizer. The synergistic composition for water soluble fertilizer comprises the following raw materials in percentage by weight: 10%-20% of L-arabinose, 10%-20% of D-galactose, 4%-6% of L-Rhamnose, 4%-6% of D-glucuronic acid, 15%-18% of glutamic acid, 25%-35% of citric acid, 10%-15% of betaine, 1%-1.2% of vitamin C, 0.1%-0.3% of vitamin B1, 0.2%-0.5% of vitamin B3, 0.1%-0.3% of vitamin B6, 0.01%-0.05% of vitamin B12. The synergistic composition for water soluble fertilizer has the effects of balancing nutrition, effectively avoiding antagonism among elements, and facilitating absorption and transportation of nutrient elements; at the same time, the synergistic composition for water soluble fertilizer has the effects of improving plant resistance, conditioning soil, and improving the utilization ratio of nitrogen, phosphorus and potassium. The synergistic composition for water soluble fertilizer has the advantages of simple production process, convenient use and favorable for large-scale popularization and application.