Bayesian equilibrium algorithm model of information vulnerability assessment was established, and it had introduced the weighted directional method in the model. Then it established an information system evaluation program for complex network, and designed the procedures of vulnerability assessment. In order to verify the validity and reliability of the model, complex network test platform was built, and the network data of the test platform was monitored. It had obtained the effect of different nodes on the network vulnerability of the complex network test platform through the calculation. It had verified the role of directed weights in the analysis of complex network, which had provided the theory reference for the vulnerability assessment of information system network.