In the current enterprise environment microbiological detection process, it is cumbersome for the operators to manually process the data, which also bring a variety of accidental errors. In the testing process, the paper form of data flow has many problems like unreasonable, non-standard, and other issues. In particular, the sharing of project information cannot be achieved between departmental operators, so that customers and operators fail to timely and accurately access to all projects progress and results. Thus, by combining JAVA language framework mature and stable advantages, this study develops a workflow-based microbiological detection system for regulating processes and information sharing. First, it designs a set of workflows that conform to the enterprise microbiological testing process in this system. Then, it uses the Bootstrap framework to design front-end pages and limit the key data. Finally, by combining Struts and the Spring framework, it develops background business processes. The whole system is rigorous and stable in structure, and the operators can easily obtain all projects' information, which greatly improves the efficiency and accuracy of microbiological detection and brings economic benefits.