In this paper, we present an agent- aware computing based collaborative information sys- tem scheme for MR applications. The HCI issues in VR, AR, and MR, have been discussed firstly. Besides the equipment, the lack of understanding of users also ac- counts for a significant bottleneck of improving user ex- perience and immersion during the interaction. Aiming at the issues, an agent-aware computing based scheme is proposed and implemented. The corresponding sys- tematic scheme is presented in the views of functional- ity, modules and system workflow and discussed in de- sign, implementation, and system synthesis. By means of the human-aware computing, system-aware comput- ing and human-system aware computing, issues such as mixed reality fusion, QoE-QoS management, confiden- tiality, and security, are addressed by the applying agent- aware computing based scheme into an implementation of the collaborative information system for mixed real- ity. Related modules along with their function and test results are given and discussed.