The convergence of Internet of Things (IoT) technologies and smart manufacturing is transforming industrial ecosystems through real-time automation, predictive analytics, and cyber-physical system integration. However, the complexity of interconnected devices introduces new governance challenges relating to security, interoperability, privacy, ethics, compliance, and system resilience. This research article develops a comprehensive IoT Governance Theory tailored for smart manufacturing ecosystems. Drawing on socio-technical governance principles, cyber-physical systems management, and digital industrial policy, this paper proposes a Multi-Layer IoT Governance Framework (MLIGF). The study identifies technological, organizational, and environmental governance dimensions and presents strategies for ensuring accountability, transparency, and operational integrity. The findings provide theoretical grounding for policymakers, industry leaders, and researchers seeking to manage IoT-enabled manufacturing ecosystems responsibly and sustainably.