The invention discloses an online parallel configuration system and method based on database interface layer operation flow and used for SCD (substation configuration description) files. When the system and the method are applied, SCD files of the whole station are analyzed firstly, IED (intelligent electronic device) models and communication subnets are mapped into an IED database and a communication subnet database, an interface layer is established on a database layer, an interface function is set, a configuration operation interface is arranged on an application layer, so that a user can input configuration commands and configuration parameters through the configuration operation interface, the databases are accessed and modified through the interface function provided by the database interface layer, and the SCD files are configured on the basis of the mapping relation between the databases and the SCD files. During parallel configuration, modification of IED files by the user is processed sequentially in an operation flow manner, data in the databases is modified one by one, and a modification result is returned to a configuration slave through the interface function. With adoption of the system and the method, collaborative configuration of the SCD files by multiple users can be realized, configuration conflict is avoided, configuration efficiency is increased, and configuration errors can be reduced.