The invention provides high-phosphorus, high-zinc and high-magnesium liquid compound fertilizer. The high-phosphorus, high-zinc and high-magnesium liquid compound fertilizer is prepared from the following raw material components in parts by weight: 3-15 parts of zinc fertilizer, 4-16 parts of magnesium fertilizer, 16-75 parts of phosphorus fertilizer, 1-15 parts of urea, 0.5-8 parts of potassium fertilizer, 0.5-4 parts of cosolvent, 0.5-4 parts of stabilizer and 10-40 parts of water. The invention also provides a preparation method and an application method of the high-phosphorus, high-zinc and high-magnesium liquid compound fertilizer. The high-phosphorus, high-zinc and high-magnesium liquid compound fertilizer has the advantages that the total nutrient content is high, physical and chemical shapes are stable, phosphorus, zinc and magnesium are stably dissolved in liquid at the same time, phenomena such as crystallization, sedimentation, layering and the like are not caused under high temperature, low temperature and normal temperature conditions, liquidity is good, nutrients are highly enriched, the high-phosphorus, high-zinc and high-magnesium liquid compound fertilizer is applicable to automatic fertilization operation in a relatively large area, fertilization efficiency can be obviously improved, foliar application and drenching can be realized, and the high-phosphorus, high-zinc and high-magnesium liquid compound fertilizer also can be applied to a spray irrigation and drop irrigation system, is easy to use, is time-saving, labour-saving and fertilizer-saving and is quick in fertilizer effect.