Complex media environment which is composed of micrometer-level microorganism aggregated particle swarm has great impact on laser transmittance. To study what the impact is, based on fractal theory, a cluster-cluster aggregation (CCA) model is used to simulate the fractal structure of microorganism aggregated particles, and the single scattering extinction parameters for aggregated particles are calculated using the discrete dipole approximation (DDA) method. Then the transmittance of 10.6 μm laser in microorganism aggregated particle swarm is studied with the Monte Carlo method. The results show that when each aggregated particle contains 20~50 original particles, the radius of original particle is 1.5 μm , the density of aggregated particles is higher than 800 /cm3 , and the porosity is less than 0.9, the transmittance of 10.6 μm laser in the microorganism aggregated particle swarm which has a 4 m-thick measurement area can be less than 10%.