The invention discloses a computer software system for processing a diagnosis process. The problems of narrow medical process coverage, nonstandard and abnormal properties of the present system are solved. The computer software system comprises a workflow file input module, a moveable execution control module, an output interface module, a workflow file analyzing module, a workflow instancing module, an engine interactive and managing module and an engine scheduling and executing module. The computer software system for processing the diagnosis process is connected with an external client through a distributed network; the workflow instancing module, the moveable execution control module, the engine interactive and managing module and the engine scheduling and executing module are utilized to schedule the execution of the diagnosis process; the workflow file input module and the workflow file analyzing module are utilized to introduce and analyze the workflow; the output interface module is utilized to outward output process executing data. The computer software system combined with the clinical pathway, the workflow engine and the rule engine can supply wide-coverage and standard diagnosis process control and management to medical personnel.