For the optimization design and flexible production requirements of work stations for complex assembly lines in manufacturing enterprises，a solution based on the directed net theory is proposed． Firstly，combining with a simple example of assembly line balancing problem， it shows that the flow chart of assembly line satisfies the features of directed graph and is represented by directed graph matrix，which converts complex network graph information into computable data and realizes the assembly line of computer calculation and program design． Secondly，assembly line with 29 nodes is taken as an example; the mathematical model of assembly line balancing problem is established with the minimum time loss of assembly line as the optimization objective，under the constraint of the time，cycletime and precedence of job elements． At last， the balancing problem of assembly line and the design of U assembly line are calculated by the use of the network theory of directed graph and line balance rate reaches 93. 81%，which verifies the rationality and validity of the directed net theory to solve the assembly line balancing problem and realizes the calculation of computer program，which provides a new method for automation design of largescale assembly line equipment in manufacturing enterprises．