Bioleaching of silicon is considered a promising strategy for fly ash resource utilization; however, its efficiency still needs improvement. In this study, a co-culture system with Bacillus subtilis and Cystobasidium sp. (1:1) was constructed by antagonistic and flask leaching experiments, which reached the growth stable phase earlier and maintained it for a longer duration compared to pure cultures. In the fly ash leaching experiments, co-culture exhibited a lower pH, and a silicon dissolution of 1.716 and 1.979 times higher than pure cultures under the optimum conditions of initial pH of 7, pulp density of 1%, and stirring rate of 150 rpm. Metabolite analysis showed that the co-culture system rapidly produced sufficient amounts of extracellular polysaccharides at the early leaching stage and maintained high yields of vital organic acids (lactic, acetic, and propionic acids) throughout the leaching process compared to the pure culture. In addition, SEM-EDS and XRD analyses showed that in co-culture system, a large number of microorganisms attached to the mineral surfaces, more destruction of the silicate minerals, and a facilitated dissociation of silicon. This should be the first investigation of silicon bioleaching by co-culture with bacteria and fungi.