The invention belongs to the technical field of microbial fermentation, and provides a micro-ecological compound microbial agent and a method for processing a solid crop culture medium through the micro-ecological compound microbial agent for solving the problems that an existing culture medium cannot be reused, and if the culture medium is reused, continuous cropping obstacles are prone to being caused, and the culture medium becomes a carrier of soil-borne disease pollution and concentrated spread. The micro-ecological compound microbial agent is prepared by mixing bacillus amyloliquefaciens LH-1, bacillus licheniformis, pseudomonas cichorii, propionigenium modestum, thermotoga aritime, bacillus stearothermophilus, candida tropicalis, trichoderma harzianum, streptomycete, actinomyces meyeri and frankiaceae according to a certain ratio. According to the micro-ecological compound microbial agent and the method for processing the solid crop culture medium through the micro-ecological compound microbial agent, pathogenic bacteria can be effectively killed, and the continuous cropping obstacles are overcome; the mode that biological and physical measures are combined is scientifically applied to solve the problems existing in reuse of the matrix, the fruit and vegetable quality safety and zero pollution to the environment are guaranteed, the production cost of farmers is lowered, the agricultural product quality safety is guaranteed, and the ecological environment is protected; the culture medium can be reused for many times, and the growth and development of crops cannot be influenced.