The invention discloses a computation cloud platform-based microbial diversity interaction analysis system and method thereof. The system comprises a project management module, a basic analysis task submission module and an interactive result analysis module. The method comprises the following steps of: firstly uploading sequencing data to a local cluster server, establishing a project in the project management module, uploading a database of customers to the local cluster server or selecting to use an online database, and locking the project in the project management module or sharing the project to other users to be operated; in the basic analysis task submission module, carrying out parameter analysis on the sequencing data by a user through a visual interface and generating a project file after the analysis; before the analysis, judging whether data quality control is qualified or not, if the judging result is positive, carrying out the parameter analysis, and otherwise, directly returning an error; and transmitting the generated project file to the interactive result analysis module to carry out interactive analysis until an intuitively displayed report is obtained.