The present disclosure provides a method, an apparatus and a system for multi-module scheduling, capable of solving at least one of the problems associated with the multi-module scheduling technique in the related art, i.e., inconsistency in data inputted to a computing module, and a significant delay or low throughput in data transmission between computing modules. The method includes: reading, by a master process, a pre-stored configuration file storing a directed computation graph; initializing, by the master process, states of the nodes and connecting edges in a current computing period; determining a node to be called based on the computation direction of the directed computation graph and the states of the nodes, the node to be called comprising a node having all of its input edges in a complete state; transmitting, to the computing module in the slave process corresponding to the node to be called, a call request of Remote Process Call (RPC) to execute the computing module; updating the state of the node and the state of each output edge of the node upon receiving a response to the call request; and proceeding with a next computing period after determining that the states of all the nodes in the directed computation graph have been updated.