The invention discloses a multidisciplinary collaborative optimization flow modeling and scheduling method and a system based on a business process execution language (BPEL). The method includes the steps of creating multidisciplinary optimization flows based on the BPEL, analyzing flow modeling files, creating multidisciplinary optimization design flow instances, executing the multidisciplinary optimization design flow instances, recording journal files of the multidisciplinary optimization flows in an iterative process, and providing checking service for the journal files. The system comprises a flow creating module, a flow analyzing module, a flow operation instance creation module, a flow instance execution module and a flow execution journal recording module. The method and the system are service-orientated in operation scheduling, support service call among networks, combine with current cloud computing well, can shield modeling principles, modeling forms and input-output inconsistency of different disciplines in modeling, and construct the single-stage and multi-stage multidisciplinary optimization flows rapidly.