The spread of microorganisms in the air, especially pathogenic microorganisms, seriously affects people’s normal life. Therefore, the analysis and detection of airborne microorganisms is of great importance in environmental detection, disease prevention and biosafety. As an emerging technology with the advantages of integration, miniaturization and high efficiency, microfluidic chips are widely used in the detection of microorganisms in the environment, bringing development vitality to the detection of airborne microorganisms, and they have become a research highlight in the prevention and control of infectious diseases. Microfluidic chips can be used for the detection and analysis of bacteria, viruses and fungi in the air, mainly for the detection of Escherichia coli, Staphylococcus aureus, H1N1 virus, SARS-CoV-2 virus, Aspergillus niger, etc. The high sensitivity has great potential in practical detection. Here, we summarize the advances in the collection and detection of airborne microorganisms by microfluidic chips. The challenges and trends for the detection of airborne microorganisms by microfluidic chips was also discussed. These will support the role of microfluidic chips in the prevention and control of air pollution and major outbreaks.