The present invention provides a second operation management system online defect diagnosis method. Starting from relay protection second device defects and second operation management system real-time defects, based on the defect management of multivariate abnormal big data analysis, alarm information requiring participation in the diagnosis is put into a defect alarm mapping queue according to the defect automatic diagnosis rule, and the defect management template of a defect management module is configured to perform detailed classification, confirmation and processing of the defects. The second operation management system online defect diagnosis method can allow the defect elimination work to be more standard and timely, is more convenient and rapid for query and analysis of the defect conditions, and the second operation management system online defect diagnosis method is applied to the relay protection operation maintenance work to greatly alleviate the operation maintainers' work and has high practical values.