The invention discloses a eukaryotic parameter-free transcriptome interactive analysis system and method based on a cloud computing platform. The system comprises a project management module, a basic analysis task submission module and an interactive result analysis module. The method comprises the steps that firstly, sequencing data is uploaded to a local cluster server, a project is built in the project management module, meanwhile, a database of a client is uploaded to the local cluster server or an online database is selected, and project locking operation or the operation of sharing with others can be conducted in the project management module; then, in the basic analysis task submission module, a user can conduct parameter analysis on the sequencing data through a visual interface, and a project file is generated after analysis; before the analysis, whether the data quality control is qualified or not is judged first, and if yes, the parameter analysis is conducted; if not, the sequencing data is directly returned, and an error is reported; the generated project file is transferred to the interactive result analysis module for interactive analysis, and a visually presented report is obtained.