A cyber-physical system (CPS) integrates communication and automation technologies into the operational processes of physical systems. Nowadays, as a complex CPS, an intelligent connected vehicle (ICV) may be exposed to accidental functional failures and malicious attacks. Therefore, ensuring the ICV’s safety and security is crucial. Traditional safety/security analysis methods, such as failure mode and effect analysis and attack tree analysis, cannot provide a comprehensive analysis for the interactions between the system components of the ICV. In this work, we merge system-theoretic process analysis (STPA) with the concept phase of ISO 26262 and ISO/SAE 21434. We focus on the interactions between components while analyzing the safety and security of ICVs to reduce redundant efforts and inconsistencies in determining safety and security requirements. To conquer STPA’s abstraction in describing causal scenarios, we improved the physical component diagram of STPA-SafeSec by adding interface elements. In addition, we proposed the loss scenario tree to describe specific scenarios that lead to unsafe/unsecure control actions. After hazard/threat analysis, a unified risk assessment process is proposed to ensure consistency in assessment criteria and to streamline the process. A case study is implemented on the autonomous emergency braking system to demonstrate the validation of the proposed method.