In view of the uncertainty of the indexes of target protection scheme as well as the inconsistency among indicators, an optimization design method based on Pareto optimal of multi objective decision making (MODM) is put forward. Combined with the practicalities of information based strategy, an evaluation index system for the target protection that meets the requirements of cyberspace confrontation is constructed. A mathematical model of protection scheme design is established. On this basis, the conductor acts upon his own preference to the weighting methods for obtaining a satisfactory solution to the optimization method. The model simulation test proved that the application of Pareto optimization of MODM narrows the decision range, achieves the purpose for improving the solution quality and benefits for the conductor to make scientific, reasonable and accurate decisions.