Interoperability is the key target of integrated architecture design, as well as the basis of the capability of integrated systems. Since interoperability plays an important role in fulfilling operational missions, this study proposes a quantification measurement method for the interoperability at architecture level by matching the missions with the initial conditions of executable model—Petri Net. First, the process net of the Petri net model is used to present the interoperation relationship between systems. Then the quality attribute for interoperation is assigned by incident matrix of system interoperation to accomplish the measurement on the interoperability of a heterogeneous set of integrated systems. Finally, the National Missile Defense System is taken as an example to illustrate the application of this method.