The invention relates to a compound microbial fertilizer having high nutrient content and a preparation method thereof; and the compound microbial fertilizer is prepared by effectively combining an inorganic nutrient, an organic matter and a microbial strain, carrying out disperse coating on the inorganic nutrient by adding kaolin, humic acid and the like in a pelletizing process, then, spraying polyglutamic acid outside particles to envelop, and adding the compound microbial strain adsorbed by a carrier. By means of the method, the compound microbial fertilizer has higher inorganic nutrient content; the effective viable count cannot be influenced; the compound microbial fertilizer having high nutrient content, disclosed by the invention, has an obvious yield-increasing effect; the disadvantage of being slow in fertilizer efficiency of the ordinary microbial fertilizer is overcome; and simultaneously, the compound microbial fertilizer disclosed by the invention has the important functions of improving soil property, increasing soil fertility, promoting plant growth, improving the quality of crops, increasing the disease resistance of the crops and the like.