The invention discloses a microbiological inoculation device and a method for treating micro-polluted water by the microbiological inoculation device, and relates to the technical field of microbiological inoculation. The microbiological inoculation device comprises an ozone aeration tower, an industrial ozone generator, a porous ceramic catalyst unit, an ultraviolet catalyst unit, an inoculant tank, a culture solution tank, an inoculation biology filtration column, an air bottle and a biological filter chamber, an aeration tray is arranged at the inner bottom of the ozone aeration tower, the industrial ozone generator is communicated with the aeration tray in the ozone aeration tower, an outlet in the bottom of the ozone aeration tower is communicated with an inlet of the porous ceramic catalyst unit, an outlet of the porous ceramic catalyst unit is communicated with an inlet of the ultraviolet catalyst unit, and an outlet of the ultraviolet catalyst unit is communicated with a water pump I. The method includes the steps: firstly, ozone ultraviolet catalysis; second, bacterial inoculation and biodegradation treatment. The method solves the problems that nutrient substances in the micro-polluted water are insufficient, inoculated bacteria are easily affected by indigenous bacteria, and the method is used for treating the micro-polluted water.