This review discusses the advancements in integrated multi-omics analysis for drug-target identification. As an essential component of modern drug discovery, drug-target identification plays an increasingly important role. While single-omics technologies have been widely used in drug target discovery, they are limited in explaining the causal relationships between drugs and complex phenotypes. With the progress of large-scale sequencing and high-throughput technologies, the trend in drug-target identification has shifted towards integrated multi-omics techniques, gradually replacing traditional single-omics techniques. This review focuses on recent advancements in integrated multi-omics techniques for target identification, highlights common multi-omics analysis strategies, briefly summarizes the selection of multi-omics analysis tools, and explores the challenges of existing multi-omics analyses, as well as the applications of multi-omics technology in drug-target identification. The review begins with an introduction to the importance of drug-target identification in drug development. It discusses the development history of omics technologies, including genomics, transcriptomics, proteomics, and metabolomics. The review then explores the advantages and limitations of single-omics analysis, such as genomics, transcriptomics, proteomics, and metabolomics. It also discusses the integration of multi-omics data, including transcriptome and proteomics, transcriptome and metabolomics, and proteomics and metabolomics. The review further summarizes the latest advancements in multi-omics technologies for drug-target identification, such as single-cell multi-omics and spatial multi-omics. It also reviews commonly used tools and databases in multi-omics technologies. Finally, the review discusses the challenges of multi-omics analyses and their future prospects for drug-target identification, with a focus on the integration of transcriptome and proteomics.This review discusses the advancements in integrated multi-omics analysis for drug-target identification. As an essential component of modern drug discovery, drug-target identification plays an increasingly important role. While single-omics technologies have been widely used in drug target discovery, they are limited in explaining the causal relationships between drugs and complex phenotypes. With the progress of large-scale sequencing and high-throughput technologies, the trend in drug-target identification has shifted towards integrated multi-omics techniques, gradually replacing traditional single-omics techniques. This review focuses on recent advancements in integrated multi-omics techniques for target identification, highlights common multi-omics analysis strategies, briefly summarizes the selection of multi-omics analysis tools, and explores the challenges of existing multi-omics analyses, as well as the applications of multi-omics technology in drug-target identification. The review begins with an introduction to the importance of drug-target identification in drug development. It discusses the development history of omics technologies, including genomics, transcriptomics, proteomics, and metabolomics. The review then explores the advantages and limitations of single-omics analysis, such as genomics, transcriptomics, proteomics, and metabolomics. It also discusses the integration of multi-omics data, including transcriptome and proteomics, transcriptome and metabolomics, and proteomics and metabolomics. The review further summarizes the latest advancements in multi-omics technologies for drug-target identification, such as single-cell multi-omics and spatial multi-omics. It also reviews commonly used tools and databases in multi-omics technologies. Finally, the review discusses the challenges of multi-omics analyses and their future prospects for drug-target identification, with a focus on the integration of transcriptome and proteomics.