In recent years, with the rapid growth of the traditional edible fungus industry all over China, the pollution and the hazard generated to the entironment and the edible fungus industry per se by a large number of obsolete fungus sticks (slags) after the primary planting of edible fungi also become bigger and bigger, and the innocent treatment and the research development in the aspect of reutilization of the obsolete fungus sticks in the industry also become more and more, wherein the research of preparing the water purifying microbial inoculum by taking the obsolete fungus sticks as the main materials is an important research direction. The invention provides a method taking the obsolete fungus sticks after the edible fungi are planted as the main materials to ferment water purifying bacteria to prepare the water purification agent. In the invention, the obsolete fungus sticks and the fungus slags of the edible fungi are used as the main materials, wherein the weight proportion is higher than 50 percent, and then the main materials cooperate with other auxiliary materials, wherein the auxiliary material mixture ratio is simple and varied; then independently developed compound water purifying freeze-drying strains are adopted to be fermented, and thereby, the water purifying bacterium is prepared. The invention reduces the preparation cost, realizes the deep development and utilization of wastes, also reduces the pollution to the entironment and eliminates the pollution of the edible fungus planting industry. The invention can realize use and preparation and has simple operation, low cost, high product activity and good water purification effect.