The invention provides a metadata model based function block diagram online debugging method. The method includes a) packaging typical real time data point and related essential properties thereof inan industrial control process into a metadata model having a uniform structure; b) based on the metadata model, defining and realizing different kinds of function blocks; c) introducing primitive information elements of the different function blocks on the basis of control command sets and metadata sets; d) generating an algorithm configuration file based on the above configuration file structureby configuration software and implementing an online monitoring function in online debugging through downloading and running the algorithm configuration file in an industrial controller and reading the metadata sets in the algorithm configuration file periodically; e) implementing an online value setting function through modifying the metadata sets by the configuration software. By adopting the method provided by the invention, communication efficiency is improved, safety of real time control data is improved and great convenience is provided for online real time debugging of control strategies.