The invention relates to a liquid compound biological fertilizer with long shelf life as well as a preparation method and application thereof. The liquid compound biological bacterial fertilizer comprises the following components in parts by weight: 2-5 parts of microbial thalli, 80-130 parts of compound nutrients, 10-30 parts of thalli protective agents and 0.5-3.0 parts of additives, wherein the microbial thalli is metered in terms of the wet weight of deposition obtained after fermentation liquor is centrifugalized, the microbial thalli include bacillus thuringiensis, bacillus megaterium, bacillus mucilaginosus and bacillus amyloliquefaciens, and the total viable count achieves 5*10<8>-5*10<9>/mL. The liquid compound biological bacterial fertilizer disclosed by the invention can be used as a biological pesticide, can be directly applied to the spraying of plant surfaces or applied to seed soaking, root irrigation, and the like, has the effects of insect resistance, phosphate solubilization, potassium solubilization, organic matter solubilization, pest resistance, and the like and is long in shelf life.