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The in-vehicle diagnostic and software update system, which supports remote diagnostic and Over-The-Air (OTA) software updates, is a critical attack goal in automobiles. Adversaries can inject malicious software into vehicles or steal sensitive information through communication channels. Therefore, security analysis, which identifies potential security issues, needs to be conducted in system design. However, existing security analyses of in-vehicle systems are threat-oriented, which start with threat identification and assess risks by brainstorming. In this paper, a system-oriented approach is proposed on the basis of the System-Theoretic Process Analysis (STPA). The proposed approach extends the original STPA from the perspective of data flows and is applicable for information-flow-based systems. Besides, we propose a general model for in-vehicle diagnostic and software update systems and use it to establish a security analysis guideline. In comparison with threat-oriented approaches, the proposed approach shifts from focusing on threats to system vulnerabilities and seems to be efficient to prevent the system from known or even unknown threats. Furthermore, as an extension of the STPA, which has been proven to be applicable to high level designs, the proposed approach can be well integrated into high-level analyses and perform co-design in different disciplines within a unified STPA framework.