The business ecosystem theory has developed rapidly in recent years and has become a hot topic in the field of business and management. However, the use of this concept is controversial. This study systematically reviewed literature published spanning nearly three decades from 1993 to 2022. In this paper, researchers designed an improved traceability method to retrieve literature based on data sources form Web of Science. VOSviewer and CiteSpace are adopted as two scientific atlas tools for information processing and visualization to evaluate the relationship between sub fields of business ecosystem. The findings show that the four branches of business ecosystem, i.e., innovation, platform, entrepreneurship and service, absorb theoretical ideas to varying degrees. Among them, the theoretical inheritance relationship of innovation branch is most clear, and gradually grows into the backbone of ecosystem research. Major contribution of this study is reflected in three aspects: Firstly, the improved traceability method provides a repeatable quantitative description process on the basis of significantly reducing researchers’ subjective participation. Secondly, from perspective of bibliometrics, the branch direction and key nodes of theory development are identified. Thirdly, the study helps identify the future development directions of business ecosystem, including innovation, digitalization, entrepreneurship, self-organization and the strategic transformation guided by emerging technologies.