The invention discloses a complex desulphurization system and method before coal combustion. Coal is crushed into particles and mixed with water, small bubbles are blown into the lower side of the suspension liquid of the coal particles and the water, the bubbles are attached to the surfaces of the coal particles and the surfaces of iron pyrite particles, the coal particles and the iron pyrite particles float on the water surface and cannot be separated due to the buoyancy effects of air and water, if microorganisms are added into a water solution, and the microorganisms are attached to the surfaces of the iron pyrite particles, so that the surfaces of the iron pyrite particles become hydrophilic from hydrophobic; meanwhile, the microorganisms are attached to the surfaces of the coal particles with difficulty, so that the surfaces of the coal particles still keep hydrophobic, under the drive of the bubbles in a flotation column, the coal particles float up, and the iron pyrite particles sink to the bottom, so that the coal and the iron pyrite are separated, wherein the microorganisms are thiobacillus thelloobacillus ferrooxidans which have high specifity on the iron pyrite, the thiobacillus thelloobacillus ferrooxidans can work after several seconds, and by means of the method, the treatment time can be greatly shortened.