The invention discloses a co-culture method of trichoderma atroviride and bacillus subtilis and an application of a co-metabolite obtained by the method. According to the method, the trichoderma atroviride SG3403 and bacillus subtilis 22 strains are used as co-culture objects, the inhibition rate of a co-culture fermentation liquid against fusarium graminearum is used as a response value, and thefermentation conditions such as culture temperature, a rotation speed, a pH, a corn flour content, a molasses content, a yeast powder content and a KCl content are optimized by a response surface method to obtain the following best fermentation conditions: the culture temperature is 28 DEG C, the rotation speed is 214 rpm, the pH value is 6.8, the yeast powder content is 10 g / L, and the molasses content is 27.6 g / L. The co-culture fermentation liquid cultivated by the formula provided by the invention improves the resistance to the fusarium graminearum, a substance not found in a single culture is found in the co-culture fermentation liquid, a seed coating agent prepared from the substance promotes the growth of wheat, and a novel option is provided for the development of biological pesticides and biological seed coating agents.