The invention discloses an online operation and maintenance method and system for secondary equipment in an intelligent substation. An advanced soft pressing plate application of the intelligent substation is proposed, including standard soft pressing plate design and the intelligent alarm of soft pressing plate cast and cancel anomalies. By implementing the function, the complexity and uncertainty of operation and maintenance overhaul of the intelligent substation are reduced. The sequence control operation of a protection device is proposed to realize one-button sequence control of cast and cancel protection and safety isolation. Through cast and cancel steps of a curing and protection device, the risk of misoperation in a safety process is effectively reduced. According to the invention, the technical scheme is experimented in a 220kV intelligent substation, and the operation status is great; the intelligent level of the substation is greatly improved; by considering the configuration of long-term interval intelligent device extension and putting forward the concept of a replacement device, the blackout time in the process of long-term renovation and extension is reduced; and modeling is carried out based on the IEC 61850 standard, which lays the theoretical foundation for the later implementation of the policy.