The invention relates to an agricultural fertilizer, in particular to a microbial compound fertilizer and application thereof. The microbial compound fertilizer specifically consists of a zymophyte agent and a compound fertilizer, wherein each gram of the compound fertilizer comprises not less than 0.2*108 bacterial cells; the compound fertilizer comprises the following components in percentage by weight: 5 to 15 percent of farmyard manure, 10 to 30 percent of humic acid, 5 to 8 percent of grass carbonic acid, 15 to 30 percent of nutrient and the balance of boric sludge; and the zymophyte agent is obtained by fermenting silicate bacteria, azotobacter chroococcum, actinomycetes, saccharomyces cerevisiae and rhodopseudomonas sphaeroides, wherein the silicate bacteria, the azotobacter chroococcum, the actinomycetes, the saccharomyces cerevisiae and the rhodopseudomonas sphaeroides are mixed together in a weight fraction of 1:1:1:1:1. The microbial compound fertilizer acting on a big field can increase the yield of crops by 20 to 30 percent, and simultaneously can obviously increase the percentage of fertile fruits, reduce fruit dropping and overgrow the fruits; besides, the maturation stage is shortened by 5 to 7 days, the yield-increasing effect is obvious, and simultaneously, the microbial compound fertilizer can obviously improve the appearance, the mouthfeel, the color and luster and the like of products, improve the quality by 1 to 2 grades, and prolong the product freshness date.