The invention discloses a functional microbe embedded slow-release composite filling material. The functional microbe embedded slow-release composite filling material comprises the following raw materials in parts by weight: 15 to 25 parts of functional microbe loaded carrier, 5 to 10 parts of thoroughly-decomposed plant fibers, 15 to 20 parts of pearlite, 10 to 20 parts of calcium carbonate, 15 to 20 parts of cement, 1 to 5 parts of kaolin and 25 to 35 parts of an adhesive. The invention also discloses a preparation method of the filling material. The preparation method comprises the following steps of: preparing an organic carrier, and inoculating functional microbes subjected to screening and acclimatization onto the organic carrier to construct the functional microbe loaded carrier; and uniformly mixing the functional microbe loaded carrier, the thoroughly-decomposed plant fibers, the pearlite, the calcium carbonate, the cement and the kaolin, adding the adhesive into the mixture, uniformly stirring, and thus obtaining the functional microbe embedded slow-release composite filling material. The functional microbe embedded slow-release composite filling material prepared by the method can improve the structural stability of the filling material, and has functions of slowly releasing nutrients and adjusting the pH. According to the functional microbe embedded slow-release composite filling material and the preparation method thereof, materials are easily available, the raw material cost is lower, the manufacturing process is simple, and industrial production can be implemented easily.