The invention provides a microecological feed additive capable of improving the eggshell quality and an application method thereof. The microecological feed additive comprises the following components: bacillus subtilis, bacillus natto, clostridia butyricum, lactobacillus metabolites, lactobacillus activators and carriers. By adopting the microecological feed additive, the microecological flora balance of laying poultry can be adjusted, the oviduct inflammation of the laying poultry can be reduced, and the calcium-phosphorus ratio in the blood of the laying poultry can be adjusted. Compared with similar additives, the microecological feed additive has the advantages of high effectiveness, good specificity, no residues and no side effects. When the microecological feed additive is used, the eggshell quality can be improved.