A core challenge in biomedical and life science research is to decipher cell-to-cell differences under pathological progression or external perturbation. Microfluidics-based integrated systems serve as powerful tools for accurately investigating cellular phenotypes and molecular responses in the state of physiological and pathological processes at the single-cell scale. Here, we review the advanced microfluidic strategies for single-cell research relevant to tumorigenesis and evolution, immune responses, and drug discovery. The review will discuss the design of microfluidic devices for single-cell analysis, the current methods of microfluidic devices for single-cell isolation, and applications of microfluidics-based single-cell analysis in cell biology, disease diagnosis, and therapy. Specifically, we will focus on the microfluidics-based techniques for single-cell operation and recent strategies for single-cell measurements. Limitations and future perspectives of microfluidics-based single-cell analysis will also be discussed.