The invention discloses a functional biological compound fertilizer and a preparation method thereof. The functional biological compound fertilizer is prepared from the following raw materials: pyrroloquinoline quinine, an aphanamixis plant extract, a microbial agent, medium elements, namely nitrogen, phosphorus and potassium, and trace elements, namely calcium, magnesium, sulfur, zinc, boron and molybdenum. The aphanamixis plant branch and leave extract is prepared by the steps of soaking fresh branches and leaves of aphanamixis plants, then sterilizing, cleaning, chopping, grinding into thick liquid, juicing, concentrating, carrying out vacuum drying, granulating and the like. The extract is rich in various amino acids, high-quality plant protein, multiple organic trace elements, multiple active enzymes, superoxide dismutase (SOD) and multiple chelates, thus being capable of carrying out effective, multi-mechanism and complementary cooperation with the pyrroloquinoline quinine, and promoting the absorption of plants. Furthermore, the soluble fibers in the plant extract have a curing action with the pyrroloquinoline quinine, so that effective components are further dispersed, and the long-acting effect of the fertilizer is further improved.