The invention discloses a fertilizer with biological ferment and a preparation method and a use method thereof. The fertilizer includes activator and nutrient, the activator is dry powder preparation of protein raw materials, water-soluble nitrogen, water-soluble phosphorus, water-soluble kalium and strain mixed fermentation products, and the nutrient is dry powder preparation of amino acid type raw materials, mineral composition type raw materials, trace element type raw materials and strain mixed fermentation products. The fertilizer can be applied by the step of primarily adding the activator into a simple fermenting container for fermentation and adding the nutrient for fermentation later. The invention can be suitable for various types of crops, can obtain the satisfactory effect after the application and has 10 times of the application effect of the traditional biological ferment fertilizer, and is beneficial to the massive popularization because the dry powder preparations with two components are suitable to long distance transportation and operations of post dry powder preparation mixing and fermentation are simple and easy.