Complicated information system (CIS) contains many inhomogeneous applications which require security, interoperability, extensibility. The paper presents a secure CIS architecture model to conduct the construction or reconstruction of CIS. Using layered method, it divides CIS into modules and reduces system complexity. Web service technology is widely adopted in layers to fulfill interoperability and extensibility. It uses encryption support layer, security protection and reliability support layer to guarantee system security and stability in different aspects. It uses system management layer to make CIS administrable. It suits highly security-critical environment such as government and bank. Been properly simplified, it can be applied to relative simple information system too.