Objective The rapid development of the agricultural economy and animal disturbance can cause exogenous microorganism-wide transmission via food chains and environmental media. This can disturb the soil native community which might trigger microbial invasion and pollution.Method Based on the core collection database of the Web of Science, we conducted a bibliometric analysis to explore the research progress of microbial invasion by using the CiteSpace knowledge map analysis tool, VOSviewer visual analysis software and HistCite citation analysis tool.Result The results described as follows: (1) During the period between 2000 and 2021, the number of research articles addressing the topic of microbial invasion increased, and attracted increasing attention; (2) The United States, China, Germany, India, and Australia were the main contributors of academic articles in the field, and also established close collaboration with each other in recent years; (3) The co-occurrence analysis of keywords showed that microbiome and metagenomic were the top two research hotspots in this field in recent 20 years; (4) "Soil Biology & Biochemistry", "Frontiers in Microbiology", "PLoS One", "Plant and Soil" and "Applied Soil Ecology" were the top five journals in this field. Among the top 10 important papers on microbial invasion, keywords of papers were clustered into 3 parts: interaction between invasive microbes and indigenous microbial communities (Cluster 1); soil microbial invasion mechanism and influencing factors (Cluster 2); impact of soil microbial invasion on the plant (crop) phenotype and disease prevention and control mechanisms(Cluster 3); (5) The rapid development of high-throughput sequencing and metagenomics made the microbial invasion a research focus; (6) The future research in microbial invasion mainly focused on the interaction between microbial invader and specific resident species, and exploration of suppression mechanism to prevent and control pathogenic microbes.Conclusion This study demonstrates the various functional exogenous microbes with the potential to disturb the balance of native communities based on bibliometric analysis. The knowledge of soil native communities and exogenous invasive microbes have been widely explored due to the rapid development of high-throughput sequencing technology. Most researchers focused on the pathogenic microbes invading the soil ecosystem rather than beneficial microbes. This is because beneficial microbial invasion can effectively prevent soil-borne diseases, promote plant growth and remediate soil pollution, while pathogenic microbial invasion can cause a decline in crop yield, and even threaten animals' health through the food chain. Thus, this study draws attention to microbial invasion; both of artificially defined beneficial and pathogenic microbes, to enhance the understanding of soil microbial balance and health and to provide important support for soil health and green agricultural production.