Diet related studies are critical in animal ecology, and diet analysis methods have been continuously improved and updated due to technical and application limitations of the different methods. The high-throughput sequencing (HTS) technique is being used to investigate the diets of wildlife. This use has greatly improved the efficiency and broadened the range of its application to diet analysis. HTS has obvious advantages of improved dataset analysis, sensitivity, and resolution, but HTS-based diet analysis is still a weak research field because it involves many different steps and is influenced by complex factors. In this study, we summarize the general strategies adopted for diet analysis using HTS, review the current progress of this technique in analyzing diet components, and elucidate the intra-specific and inter-specific dietary relationship and the relationship between food resources and habitat and behavior. Then the influences of PCR bias, contamination, and quantitative analysis on accurate diet analysis are discussed. Ways to improve the technique are proposed, as are the prospects for the future application of this method.