Inattention to the security of Web-service based software systems has more damage results and using of them has harmful consequences, due to this kind of software systems have most important security challenges. So far, security standards by traditional security mechanisms, such as encryption and digital signatures for security of Web service based systems have been discussed. The classical techniques of fault tolerance, the conventional method to enhance the security of Web services security are exploitable. In spite of the security standards and techniques were mentioned, so far have not provided complete security of Web services and we are witnessing the continuing influence. Whereas traditional security mechanisms and techniques could not respond the security requirements of Web services, so "intrusion tolerance technology" that means continuing delivery of services in presence of attack is a fundamental approach for increasing the security of Web services. In this paper, we propose a new approach for intrusion-tolerant Web services design, based on combination of fault-tolerance techniques and traditional security methods with emphasis on design diversity techniques. We have modeled the proposed software design by Markov chains in two cases. In the first case, the model uses redundant components, while in the second case, the model uses non-redundant components. Then, we have solved models using Maple software. The evaluation results show that the system throughput is considerably increased in the case of using redundant components.