The invention provides a composite microbial flora and an enzyme product thereof, and a method of applying the composite microbial flora and the enzyme product thereof in soil restoration. The composite microbial flora is composed of a microbial flora and a bioactive enzyme, wherein the microbial flora is composed of bacillus subtilis, bacillus mucilaginosus, bacillus amyloliquefaciens, pediococcus pentosaceus, pichia farinose and pediococcus acidilactici, and the bioactive enzyme is composed of phytase, protein hydrolase, cellulose hydrolase and urease. Compared with the prior art, an effective microbial community and a microecological environment are constructed to realize biological catalysis and improve the content of organic matters and beneficial microbial flora in soil, and thus, the fertility of the soil is improved; biochemical degradation rate of soil pollutant can be substantially accelerated, digestion and biodegradation of the pollutant can be accelerated, and final inertial products like carbon dioxide, water and nitrogen are obtained; and toxic intermediate produced in the process of biochemical degradation can be rapidly removed, odor is eliminated, and emission of organic volatile matters (VOC) is reduced.