The invention provides a high-throughput gene sequencing big data analysis cloud platform system. The high-throughput gene sequencing big data analysis cloud platform system comprises nine functionalmodules, namely a data file management module, a sample and experiment management module, a workflow management module, an analysis task management module, a work order management module, a mobile terminal service module, a disk quota management module, a resource sharing management module and a user and authority control module. The high-throughput gene sequencing big data analysis cloud platformsystem supports cloud storage and high-performance computing clusters, achieves storage and analysis of high-throughput gene sequencing big data, and remotely manage experiments, samples and data bya WEB terminal and mobile terminal technology, remotely controls and views analysis tasks, and achieves seamless connection of a big data cloud storage system and a high-performance computing clustersystem; the high-throughput gene sequencing big data analysis cloud platform system supports online management of the gene sequencing big data, is automatic in analysis process, pushes an analysis result report, and achieves a one-stop solution of generation of the analysis report from the gene sequencing data.