A cyber-physical system (CPS) is an integration process between the cyber-world and the physical world. Because the cyber-world affects the physical world with actuators, CPS security is crucial. Limited by characteristics of low computation power and small storage capacity of embedded devices, cloud computing is enabling technology to provide computation resources. As a result of complexity and diversity in real-world activity, fuzzy logic is required for risk assessment. Therefore, developing an integrated framework for seamless security is necessary. This paper implements and analyzes an integrated framework for cultural heritage called "Banyan Tree Guardian". Banyan Tree Guardian detects intrusion and regulates growth. Physical parts consist of a sensor network involving temperature, light, humidity, and intrusion sensors. However, sensing data require computation for analyzing. This study devises a set of cloud services that collect data and control alarms, sprays, and other physical actuators. Both physical and network intrusions are crises in cultural heritage preservation. As a result, we implement fuzzy logic in physical intrusion detection, and design a cross-layer compromise detection mechanism. To verify our concept, we implement the actual CPS at the Taiwan Confucian Temple.