We analyze the generation, transmission and living mechanism of indoor airborne microbes and present two commonly used engineering control methods for microbial contamination: ventilation and air filtration. A mathematical calculation model is developed to incorporate the two ways likely having significant impact on microbial contamination control. We also discuss the relationship between different ventilation parameters and microbial concentration, provide some design equations for determination of microbial filtration efficiency, and calculate the efficiency of air filters used in certain buildings. The results show that the natural ventilation is not a good contamination control for airborne microbes when they are a main indoor pollutant; mechanical ventilation should be used in such cases. If the atmospheric airborne microbes cannot be neglected or its indoor concentration is high, incorporating ventilation with air filtration is a good way to control indoor airborne microbial contamination. Enhancement of filter efficiency at various levels used in central airconditioning systems is helpful for improving indoor microbial contamination control condition.