Mass spectrometry-based proteomics has developed rapidly, finding a method of quick, highly reproducible and accurate quantification is a great challenge in this research sphere. Quantitative proteomics as a new branch allows deeper insight into biological study. Recently, label-free quantification has been increasingly attractive for its simple sample preparation, low cost of reagents and clean results. Mass spectrometry-based label-free quantitative proteomics is generally divided into two categories, which are based on peptide chromatographic ion intensity and based on spectral counts. This review gives a general principle of these two label-free methods, presents a relatively complete summary of some commonly used label-free quantitative methods and their latest progress, and discusses the differences between the two methods and some challenges for label-free methods. We wish this review could provide a rational introduction of selecting label-free methods optimally suited to address your specific issue.