Sediment ancient DNA can trace the climate and environmental changes of its surrounding areas, which is helpful to explore the relationship among the biological diversities, climate changes and human activities. Here, metabarcoding and metagenomics of high-throughput sequencing were summarized for better understanding the different methods for sediment ancient DNA study. Compared with the metabarcoding and metagenomics, it was found that different methods were selected for the different research purposes. The research samples of ancient DNA were changed from single species to multiple species, according to the development of the sequencing technology. Now, High-throughput sequencing technology has played an important role in ancient DNA study, which is widely used for the studies of sediment ancient DNA. In this review, we summarized the research progress in different stages and some problems of sediment ancient DNA. The significance of sediment ancient DNA were shown in this work. In conclusion, both metabarcoding and metagenomics have their own advantages and disadvantages, even both of them were belonged to the high-throughput sequencing technology. So, The significance of this study is to summarize and compare the research methods of sediment ancient DNA under the high-throughput sequencing, it had guiding significance for future research.